Apostila Prática - Introdução Modelagem VMOD - WST

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CURSO BÁSICO DE MODELAGEM COM
VISUAL MODFLOW FLEX
Cursos Profissionais WST
Apostila Prática
Maio de 2021
© Waterloo Hydrogeologic Page 1 
 
 
Visual MODFLOW Flex Exercise – Intro 1 
An Introduction to Groundwater Flow and Contaminant Transport 
 
Problem Description 
The site is in an industrial park that has a leaky underground storage tank (UST) holding unleaded 
gasoline (illustrated in the figure below). The site is 200 meters by 150 meters by 30 meters deep, 
with the groundwater flow direction from left to right (west to east). 
 
Exercise Objectives 
• To create a groundwater flow model using Visual MODFLOW Flex and visually examine the 
results of your model using contours of hydraulic head, particle pathlines, and velocity 
vectors 
• Use Visual MODFLOW Flex to build a contaminant transport simulation and view the results 
using contours, color shading, and a concentration breakthrough curve from an observation 
well that you will add to the model. 
• Assign a remediation pumping well to assess the option of a pump and treat remedial 
measure. 
• Examine model results using state-of-the-art 3D graphics technology. Utilizing Visual 
MODFLOW Flex, you will create 3D volumetric shapes that represent contaminant plumes 
changing over time. 
 
 
H
e
a
d
 =
 2
6
.5
 m
 H
e
a
d
 =
 2
9
.5
 m
 
X = 200m, Y = 150m ➔ 
 X = 0m, Y = 0m 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
 
Terms and Notations 
For the purposes of this tutorial, the following terms and notations will be used. (This assumes you 
are using a right-handed mouse.) 
type - type in the given word or value 
↔ - press the <Tab> key 
 - press the <Enter> key 
 - click the left mouse button where indicated 
 - double-click the left mouse button where indicated 
Starting Visual MODFLOW Flex 
On your Windows desktop, you will see an icon for Visual MODFLOW Flex 
 Visual MODFLOW Flex to start the program. 
The following Visual MODFLOW Flex window will appear: 
 
 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
PART 1: CREATING A GROUNDWATER FLOW MODEL 
Section 1: Project Settings 
To create a new project: 
 File / New Project… from the top menu bar 
A Create Project dialog box will be displayed prompting you to enter the project name of the new 
Visual MODFLOW Flex project. 
 
 Type: Intro1 as the project name 
 Browse button under Data Repository 
 Select a directory on the hard drive (or use the default location) 
Note: By default, new Visual MODFLOW Flex projects will 
be saved to the following location - 
[C:\Users\<username>\Documents\Visual MODFLOW 
Flex\Projects] 
The default units are appropriate and do not need to be changed. 
 OK button in the lower right corner of this window 
The following window will then appear: 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
 
The Select Modeling Scenario allows you to choose whether to proceed with the Conceptual or 
Numerical modeling workflow. The conceptual modeling workflow allows you to import all data 
objects into Visual MODFLOW Flex and to build a conceptual site model (CSM). The CSM can then be 
used as a starting point for several different numerical models. In other words, numerical model (i.e. 
with different grid types, engines, etc.) can be quickly and easily created based on the same 
conceptual modeling. This makes it easy for the user to manage several different numerical models 
with slight variations. 
Conceptual modeling is not covered in this exercise, so we will proceed with the numerical modeling 
workflow: 
 Numerical Modeling 
Proceeding with the numerical modeling workflow will bring you to the first step in the that 
workflow, which is to define your model objectives. This step allows you to specify whether you will 
be running a fully saturated or variably saturated model, whether contaminant transport will be 
included, which flow/transport engines will be utilized, etc. You will see the following window open: 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
 
We will retain most of the default settings in this step, but we will change the start date: 
 Wednesday, January 1, 2014 (select from dropdown menu) 
We will keep the default flow parameter values. 
 [Next Step] proceed to the next step in the workflow 
The Define Numerical Model workflow step will appear, allowing you to select whether to import 
an existing grid or create a new one. We will create a new grid in this exercise: 
 Create Grid 
This will bring you to the ‘Create Grid’ step in the numerical modeling workflow. At this step you will 
specify the boundary/extents of your model and the structure of your model’s grid. Your screen 
should look like the image below: 
 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
 
Section 2: Define Model Grid 
Now you will specify the number of rows, columns, and layers to be used in the model. Under the 
‘Grid Definitions’ frame, enter the following model rows, columns, layers and depth information in 
the appropriate boxes: 
 Rows = 30 
 Columns = 40 
 Xmin = 0 
 Xmax = 200 
 Cell width = calculated this value can be adjusted as per project requirements 
 Ymin = 0 
 Ymax = 150 
 Cell height = calculated this value can be adjusted as per project requirements 
For this exercise, you will ignore the option “Calculate extents from a polygon object”. Next, specify 
the parameters for the vertical grid discretization: 
 Type: 10 For the Number of Layers 
Specify the layer Elevations (typing the values directly into the grid): 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
 
Layer1 - Top: 30 (replace 100) 
Layer2 - Top: 27 
Layer3 - Top: 24 
Layer4 - Top: 21 
Layer5 - Top: 18 
Layer6 - Top: 15 
Layer7 - Top: 12 
Layer8 - Top: 9 
Layer9 - Top: 6 
Layer10 - Top: 3 
Layer10 - Bott: 0 
The screen should now look like the image below: 
 
 Create Grid Click the ‘Create Grid’ button at the top-right 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
 [Next Step] proceed to the next step in the workflow 
Visual MODFLOW Flex will then construct a 40 columns x 30 rows x 10 layers finite difference grid 
with uniform grid spacing in both the X and Y directions, and will automatically create the model run 
Input tree structure. By default, you will be taken to the View Grid step as shown in the following 
image: 
 
The ‘View/Edit Grid’ portion of the workflow allows the user to make any necessary changes to the 
grid structure. This is particularly useful if you are following the conceptual modeling workflow and 
would like to test slight variations in the grid structure. Since we’ve just created this grid and do not 
require any changes we will proceed to the next step in the workflow, ‘Define Properties’. 
Section 3: Define Properties 
 [Next Step] proceed to the next step in the workflow 
Under the ‘Toolbox’ in the main working window, ensure that conductivity has been selected from 
the first dropdown menu. 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
 Conductivity from the list menu under the Toolbox 
 Edit option under the Toolbox 
The default property values will be displayed in the Conductivity dialogue box. 
 
For this simple model, we will assume all grid cells have the same hydraulic conductivity (values are 
defined in m/s) 
 Type: 2e-05 for Kx under Layer 1, Row 1, Column 1 
 (or F2) to assign this value to the entire column 
 Type: 2e-05 for Ky under Layer 1, Row 1, Column 1 
 (or F2) to assign this value to the entire column 
 Type: 2e-06 for Kz under Layer 1, Row 1, Column 1 
 (or F2) to assign this value to the entire column 
 OK to exit the dialogue window 
Now we will change the storageparameters of the model. 
 Storage from the list menu under the Toolbox 
 Edit option under the Toolbox 
Change the storage parameters as follows; 
 Type: 0.15 for Sy Specific Yield (dimensionless) 
 (or F2) to assign this value to the entire column 
 Type: 0.001 for Ss Specific Storage (1/m) 
 (or F2) to assign this value to the entire column 
 Type: 0.15 for Ep Effective Porosity (dimensionless) 
 (or F2) to assign this value to the entire column 
 Type: 0.20 for Tp Total porosity (dimensionless) 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
 (or F2) to assign this value to the entire column 
The edit property dialogue box should look like the figure below: 
 
 OK to accept these storage values 
Now is a good time to save the project. 
 File/Save Project from the main menu 
Section 4: Add Basemap 
You will select a shapefile to be used as a background base map for your model. 
 File / Import Data… from the main menu 
A ‘Data Import’ window will open, 
 Select ‘Dxf’ in the ‘Data Type’ list menu 
 […] button next to ‘Source File’, to browse to 
 the data import file 
 Browse to the location where you downloaded the 
 ‘Supporting Files’ folder 
 ‘basemap.dxf’ in your project directory 
 Open to open the data file 
 Next >> to accept default settings 
 Next >> to accept default settings 
 Finish to import the map object 
The new data object will appear as the last item in the data tree. We can view the basemap in a new 
2D Viewer window: 
 Right-click on ‘Basemap’ in the ‘Data Tree’ 
 2D Viewer from the menu 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
The basemap will become visible in a new view window which appears as a new tab. To change the 
background colour of the 2D viewer: 
 Right-click anywhere within the window 
 Background colour from the pop-up menu 
 Select: Grey 
 OK 
Your display should look like the figure below: 
 
Close the viewer window by selecting the ‘X’ in the tab labelled ‘2DViewer -1’. 
Section 5: Input of Boundary Conditions 
The following section of the exercise describes some of the steps required to assign the various 
model boundary conditions. 
Ensure that you return to the ‘NumericGrid1-Run’ tab and close the 2D viewer tab to continue. 
Assigning Constant Head 
 [Next Step] proceed to the next step in the workflow 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
To view the model grid in relation to the basemap, check mark the basemap data object from the 
tree. 
  Basemap activate the basemap by clicking from the ‘Data Tree’ 
 Right-click anywhere within the window 
 Background colour from the pop-up menu 
 Select: Grey 
 OK 
To assign a constant head boundary ensure that this boundary condition type is selected from the 
‘Toolbox’: 
 Constant Head under the toolbox 
You will use a constant head boundary to represent the heads along the east and west sides of the 
model. From the toolbox menu: 
 Assign under the toolbox 
 Polyline from the menu that appears 
You will assign a vertical line coinciding with the equipotential of 29.5 m on the left side of the 
domain. 
 Move the mouse-pointer to the upper-left corner of the grid 
 Left-click the center of the cell 
 Move the mouse-pointer to the lower-left corner of the grid (you should 
see a red line being drawn) 
 Right-click the center of the cell. A small menu will appear after 
completion of drawing the line: 
 Click Finish from the menu that appears. 
The Define Boundary Conditions dialog will appear. 
 Next >> we will keep the default name 
Enter the following values: 
 Starting head = 29.5 
 (or F2) to assign this value to the entire column 
 Ending head = 29.5 
 (or F2) to assign this value to the entire column 
Since the model is steady-state (boundary condition values do not change over time), no time values 
are required. The Define Boundary Condition window should look like the figure below: 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
 
 Finish to confirm and create this constant head 
 boundary condition 
A set of red points will now fill the selected cells, indicating that a constant head boundary value has 
been applied. 
Now assign a constant head boundary to the right (east) side of the model in a similar fashion. 
 Assign under the toolbox 
 Polyline from the menu that appears 
 Move the mouse-pointer to the upper-right corner of the grid 
 Left-click the center of the cell 
 Move the mouse-pointer to the lower-right corner of the grid (you should 
see a red line being drawn) 
 Right-click the center of the cell. A small menu will appear after 
completion of drawing the line: 
 Click Finish from the menu that appears. 
The Define Boundary Conditions dialog will appear. 
 Next >> 
Enter the following values: 
 Starting head = 26.5 
 (or F2) to assign this value to the entire column 
 Ending head = 26.5 
 (or F2) to assign this value to the entire column 
 Finish to confirm and create this constant head 
 boundary condition 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
The constant head cells on the right edge were automatically moved down to the second model layer 
(Layer 2). Visual MODFLOW Flex’s "smart" interface recognizes that the assigned head (26.5 m) is 
below the bottom of the first model layer (elevation = 27.0 m), which is not permitted by MODFLOW. 
Visual MODFLOW Flex takes care of this automatically. 
 Type: 2 under Layer to display 
You will see the line of constant head cells on the right side of the model domain. 
Now you will examine the model in cross-section to verify the location of these boundary condition 
cells: 
  Row from the list of available views 
By default, Row 1 will be shown in the cross-section view. You can see that the constant head has 
been assigned to the cells in the second layer (red cell on the right side). To view the model in more 
detail, you can apply a vertical exaggeration factor. The following screen will appear: 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
 
 
 
Assigning Recharge 
The annual recharge to the water table at the site is approximately 150 mm/year. Recharge must be 
assigned in the Layer view, specifically to Layer1. 
 □ Row from the list of available views (remove the checkbox) 
 Type: 1 under the Layer to display 
Follow the steps below specify the annual recharge in layer 1. Change the Boundary condition type 
to Recharge under the Toolbox 
 Recharge from the list of available boundary conditions 
 Assign button, under the Toolbox 
 Entire Layer from the menu that appears 
The Define Boundary Condition window will appear. 
 Next >> 
 Recharge (mm/yr) = 250 
 (or F2) to assign this value to the entire column 
 Ponding (m) = 0 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
 (or F2) to assign this value to the entire column 
 Static select this from the menu for ‘Schedule’ 
The Define Boundary Condition window should look like the figure below: 
 
 Finish to confirm and create this recharge 
 boundary condition 
Upon completion, you should see a set of white points in all the cells in layer 1, indicating that the 
cells belong to RechargeZone1; feel free to click on the Database button, to see the list of Recharge 
zones and corresponding values. 
Now is a good time to save the project. 
 File/Save Project from the main menu 
Section 6: Adding Particles 
 [Next Step] proceed to the next step in the workflow 
The next step in the workflow is to select a type of run (single or PEST run), but there are a few 
optional tasks to complete beforeselecting the run type, such as assigning tracking particles, 
ZoneBudget zones or observation wells. You will be presented with a choice screen with several 
options. 
 Define Particles 
First, turn on the basemap in the viewer window 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
  Basemap from the data tree 
You will place particles in a vertical line down-gradient of the contaminant source in order to examine 
their pathlines later. Particle pathline analysis is a useful tool in rapidly assessing the risk potential 
to down-gradient receptors from a groundwater contamination plume. 
There are several ways of assigning particles. The user can manually select points where particles 
will be placed, place a circle of particles around a single point, or use an imported data object to 
specify the origin of the particles. We will use the imported data object option in this exercise. 
First you must import the particles from XYZ points defined in an excel file. 
 File a dropdown menu will appear 
 Import Data… from the menu 
 Point from the data type dropdown menu 
 […] to browse to the correct file 
A dialogue box opens that allows you to browse for the appropriate file. In the project directory 
choose the following file: 
 Particles.xlsx 
 Open 
 Next >> from the Data Import window 
 Next >> accept the defaults in the Data Import Window 
 Next >> accept the defaults in the Data Import Window 
 Next >> accept the defaults in the Data Import Window 
 Finish 
You should see a new ‘particles’ data object appear in the data tree, in the top left corner of the 
window. 
From the main window, under the “Toolbox” 
 Assign 
 Using Data Object from the pop-up menu 
The following window will appear: 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
 
At this step, you choose the desired points data object and convert these into particles. 
 Particles select the points data object from the data tree 
 under ‘Select Point Object’ 
  Forward select forward as the particle type 
The window should appear as follows: 
 
 OK to accept the default settings and create the particles 
The particles should now appear as points, in the layer view. These are located along column 11 in 
the grid, as shown below: 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
 
Now is a good time to save the project. 
 File/Save Project from the main menu 
Section 7: Running MODFLOW and MODPATH 
You are now ready to perform the groundwater flow and particle pathline simulation by running 
MODFLOW 2005 and MODPATH. From the top of the main workflow window, 
 [Next Step] proceed to the next step in the workflow 
You will be presented with an option to Select Run Type 
 Single Run 
You will be prompted to select which engines to run. By default, MODFLOW-2005 should already be 
selected; you also need to include MODPATH in the model run: 
  MODPATH from the list of available engines 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
 [Next Step] proceed to the next step in the workflow 
The translation settings will appear; this allows you to adjust solvers and their parameters (number 
of iterations, head-change criterion, damping factors), package settings, output control, etc.. In the 
future, you might wish to increase the maximum number of iterations if the model does not 
converge. For now, we will simply use the default settings. 
The model run is setup as a steady-state simulation. You can see this defined as follows: 
 Settings under MODFLOW-2005, in the settings tree 
 Type: 3650 for steady-state simulation time 
The MODFLOW-2005 settings tree should look like the figure below: 
 
Note: The ‘Steady-State Simulation Time’ is not used if you 
have selected Transient Flow. However, a number must 
still be entered. Although the simulation will always be run 
to the same equilibrium solution in Steady State, the total 
amount of water passing through boundary conditions 
depends on the amount of time simulated. For example, 
Zone Budget analysis of a Steady State solution would be 
affected by the simulation time, whereas regional head 
values would not. 
You are now ready to create the input files (packages) for MODFLOW and MODPATH. 
 button located on the workflow toolbar 
Visual MODFLOW Flex will now create the files necessary to run the USGS MODFLOW and MODPATH 
programs. You will see a progress of the Translation, which should take approximately 5-10 seconds. 
Once complete you will see ‘Translation Finished’ at the bottom of the translation log details window. 
 [Next Step] proceed to the next step in the workflow 
 button located on the workflow toolbar 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
The numeric engines will start running and display progress in the main window. MODFLOW-2005 
will run first followed by MODPATH. Each engine will have an information window that displays 
simulation results and progress. Clicking on the tab of the respective window will enable you to view 
detailed results of each run. 
 
The model run should take approx. 10-30 seconds. Once completed, you should see a few new 
objects appear in the model explorer tree, under “Outputs / Flow” 
• Heads 
• Drawdown 
• Fluxes 
• Water Table 
• Forward Pathlines 
Section 8: Output Visualization 
 [Next Step] proceed to the next step in the workflow 
You will be presented with an option to View Results, and select the desired results type 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
 View Maps 
 
The head equipotential lines for your simulation will be displayed initially by default. 
Take a moment to review the range of calculated head values over layer 1; note that as you mouse 
over the Layer view of the grid, the values in the status bar at the bottom of the window, will display 
the X,Y position of the mouse cursor, along with the layer, row, and column for the cell and the 
calculated head value for that cell. 
Notice the olive-colored cells on the right of the model, which indicate cells that are “dry”. Dry cells 
occur when the calculated hydraulic head is below the bottom of that particular cell (thus 
representing the unsaturated zone). To better visualize and understand what is meant by dry cells, 
we will view the model in cross-section. 
  Row from the list of views 
 Type: 15 under the Row, to display row 15 
 □ Layer to remove from the list of views 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
Also, we will turn on the calculated water table location for the model. Locate the Model Explorer, 
and the items under “Outputs/Flow” in the lower right corner of the window: 
  Water Table from the model explorer tree, under Outputs/Flow 
The water table will appear as a solid blue line. 
Now decrease the Vertical Exaggeration of the Row view to improve the display: 
 Type: 5 under Exaggeration (located above the 2D View) 
We can now see the equipotential lines from 29.5 m on the left to 26.5 m on the right. Examination 
of column 38 shows that the water table near the down-gradient boundary, is located entirely below 
the bottom of Layer 1, thus causing MODFLOW to treat these cells in Layer 1 as dry. You can see that 
in the adjacent cell, Layer 1, Column 37, the calculated head is 27.1, which is just above the cell 
bottom of 27.0 m (you can see these values in the status bar by placing the mouse cursor in the cell 
to the left of the dry cell, in layer 1.) 
 
Section 9: Viewing Particle Pathlines 
To see the results of the particle tracking pathline simulation, you must set the Pathlines visible in 
the model tree: 
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Visual MODFLOW Flex Exercise:Intro1 
 
 
  Forward Pathlines from the model explorer tree, under Outputs/Flow 
This will display the pathlines of the forward tracking particles that you specified. You may scroll 
through the various rows of the model domain, by using the up/down arrows under rows. In addition, 
you may turn on the 3D view, to see the color maps of heads and pathlines. 
 
This completes Part 1 of the Intro exercise. 
In Part 2 of this exercise, you will set up and run a contaminant transport simulation using MT3DMS. 
Now is a good time to save the project. 
 File/Save Project from the main menu 
 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
PART 2: RUNNING A TRANSPORT SIMULATION USING MT3DMS 
In this section, you will simulate the transport and fate of a dissolved-phase groundwater 
contaminant plume. The evolution of the contaminant plume will be simulated for a ten-year period. 
Section 10: Setting Up a Transport Model 
 Define Modeling Objectives from the workflow tree 
In the right side of the window, you can define the settings for the Transport Model run. 
  Transport Active add a check box beside this setting 
Next you will define the sorption and reaction options. Using the settings in this window, you can: 
1. Select the desired sorption and reaction options 
2. Add and remove chemical species 
3. Set the initial concentration of those species 
4. Set transport and reactive parameters used in the transport calculations. In this example 
MT3DMS v.5.3 will be used as the transport engine. 
By default, you will be viewing the ‘Species Parameters’ tab. Under default initial concentration 
(SCONC), you will see this is set as 0 mg/L. This means that the initial concentration in every cell is 
zero. If you wanted to alter this value it could be done at this time. Otherwise you can define spatially 
distributed initial concentrations at the Define Properties step. For this simulation, you will use the 
default value of 0 mg/L. 
Section 11: Creating a Refined Grid 
Before assigning the concentration source, it is important to create a more refined grid in our area 
of interest, where predictions will be made of plume concentration. This will allow us to improve the 
accuracy of the simulated plume and therefore better predict the ultimate fate of the groundwater 
contaminant. 
Fortunately, Visual MODFLOW Flex allows us to create multiple numerical representations for the 
site, and derive the inputs for each numerical model from the conceptual objects that were 
generated while drawing the property zones and boundary conditions in Part 1 of this exercise. 
From the model explorer tree, locate the ‘Simulation Domain’ folder. Under this, find the item Model 
Domain. 
 Right-click on NumericGrid1 from the workflow tree 
 Edit Numerical Grid… from the menu that appears 
 
 
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A Grid Refinement window will appear. Enter the following values, under the ‘Grid Edit Details’ tab: 
 Type: RefineGrid for the New Grid Name 
 Type: 10 for From 
 Type: 20 for To 
 Type: 2 row(s) with 
 Apply grid edit to apply this row refinement 
Once finished, the display should appear as below. 
 
 
 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
The rows between the 2 selected gridlines will automatically double. Now, we must perform the 
same task to the columns in the model. 
  Edit Columns from the top left of the window 
Enter the following values, under the ‘Settings’: 
 Type: 10 for From 
 Type: 20 for To 
 Type: 2 row(s) with 
 Apply grid edit to apply this row refinement 
The number of columns between these 2 gridlines should automatically double. Once completed, 
your grid should look like the following figure: 
 
 OK to apply the grid edits and close the window 
Please note that a whole new file structure has been generated within the Model Explorer, as shown 
in the image below: 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
 
The new refined grid will be automatically populated with the property zones and boundary 
conditions as defined in the original model run. You will also notice that a new tab is generated 
within the Visual MODFLOW interface, named ‘RefineGrid-Run1’. This new tab contains the 
workflow associated with the new refined grid. This tab will open automatically and you should be 
redirected to the Define Model Objectives step associated with the new workflow. 
We won’t make any changes to the grid structure, so let’s proceed to the Define Boundary Conditions 
step: 
 Define Boundary Conditions from the Worflow menu 
Now is a good time to save the project. 
 File / Save Project from the main menu 
Section 12: Adding the Contaminant Source Concentration 
You are now ready to represent the contaminant source by assigning a constant concentration to 
the cell where the storage tank is located (in Layer 3). Change the Boundary condition type to 
Constant Concentration under the Toolbox 
 Constant Concentration under the Toolbox 
 Type: 3 under Layer to view layer 3 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
This is the model layer associated with the location of the leaking storage tank. We will need to view 
the basemap in order to assign the contaminant source to the correct location. 
  Basemap under the Data Tree 
You should now zoom into the storage tank area using the tools at the top of the 2D viewer window. 
 to zoom to a box 
Digitize a box around the storage tank so that this becomes more visible. 
 Left-click in the region of row 17, column 8 
 While holding the button: 
 Pan the mouse to row 24, column 15 
 Release the button. 
The viewer window should look like the following: 
 
 Assign button under the Toolbox 
 Polygon from the menu that appears 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
Assign the constant concentration boundary condition by digitizing a polygon on top of the circular 
storage tank, using the left mouse button to assign vertices where necessary. Double-click to close 
the polygon and then right-click in the polygon. A small menu will appear after completion of drawing 
the polygon: 
 Finish from the menu that appears 
The Define Boundary Condition dialog will appear: 
 
 Next >> 
 Type: 250 for Conc001, replacing the -1 value 
 (or F2) assigns this value to the entire column 
You will assume that the solubility limit will be maintained for the duration of the simulation. 
 
 Finish 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
You should see a few new points appear on top of the circle in the layer view, which indicates that 
those grid cells have a Constant Concentration boundary condition assigned to them. 
Section 13: Adding a Concentration Observation Well 
 [Next Step] proceed to the next step in the workflow 
The Select the Next Step window will appear 
 Define Observation Wells 
In order to see how the plume concentration changes over time down-gradient from the source of 
contamination, you will add a monitoring well. Later, you will use this monitoring well to assess 
plume concentration at this point by displaying a concentration versus time breakthrough graph. 
The well location must be imported from an excel file. 
 File / Import Data… from the main menu 
A Data Import dialog box will appear. 
 Well from the data type drowdown list 
 […] to browse to the correct file 
A dialogue box opens that allows you to browse for the appropriate file. In the project directory 
(C:\VMODFlex\Intro1\), choose the following file: 
 Conc_obs_well.xls 
 Open 
 Next >> from the data import window 
 Next >> in the preview window 
The followingwindow will appear: 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
 
In this window, you define what well data to import. Under the “Select the type of data you want to 
import” 
  Well heads with the following data from the top left of the window 
  Observation points 
  Observed concentrations 
Once done correctly, you should have the following options defined 
 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
 Next >> from the data import window 
 Next >> in the preview window 
 Observation points tab at the top of the data import window 
 Conc Obs. Map to field for Concentration 
 Time Map to field for Concentration observation data 
 
 Next >> in the preview window 
 Finish 
A new data object, conc_obs_well will appear in the model tree 
 conc_obs_well from the Data Tree 
 button under the Toolbox in the main window 
A concentration observation well will appear as a point down-gradient of the source area. However, 
it will be displayed in Layer 3 corresponding to the vertical observation point (e.g. screen elevation). 
 Type: 3 under Layer to change view to layer 3 
  Concentration Observations in the Model Explorer 
Since well OW-1 is an observation well, you have entered a zero concentration. If this well were used 
as a calibration point to calibrate (qualify) the results of a contaminant transport simulation, you 
would enter the actual contaminant concentrations measured at the site, over several periods of 
time. 
Now is a good time to save the project. 
 File / Save Project from the main menu 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
Section 14: Assigning Dispersion Properties 
 Define Properties option in the Workflow tree 
 Change the Parameter group to Dispersion under the Toolbox 
 Longitudinal Dispersion from the menu under Toolbox 
 Edit… 
Change the default Dispersion to 2.0. 
 Type: 2.0 in the Dispersion column 
 (or F2) assigns this value to the entire column 
 
 OK 
The ratio of the horizontal and vertical dispersivity to the longitudinal dispersivity has default values 
assigned for this model; default value for Horiz/Long. Dispersivity is 0.1; default value for Vert./Long 
Dispersivity is 0.01. These values are assigned for all layers in the model and do not need to be 
adjusted for this exercise. 
Section 15: Running MT3DMS 
You are now ready to run MT3DMS. Navigate to the Single Run step in the workflow, 
 Single Run option in the Workflow tree 
  Run Transport Engine to include this engine in the model run 
 Select MT3DMS from the transport engine dropdown menu 
 [Next Step] proceed to the next step in the workflow 
 Settings under the MODFLOW-2005, in the Settings Tree 
 Type: 3650 for Steady-state simulation time 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
Next setup the MT3DMS option 
 General under MT3DMS, in the Translation settings tree 
The first line contains the Porosity options. By default, the “Effective” porosity option is selected. 
 Total for the Porosity option 
MT3DMS allows you to select the solution method for the advection component of the transport 
equation. Depending on the situation, each solution method presents advantages and 
disadvantages. For this exercise, you will select the Upstream Finite Difference, which based on trial-
and-error has proven to reduce the amount of numerical dispersion in this exercise. 
 Solution Method under MT3DMS, in the Translation settings tree 
 You will see the Solution Method settings on the right side of the window. 
 Yes for the Use Implicit GCG Solver 
Although the flow field is steady-state, you will run a transient transport simulation to see the 
evolution of the plume with time. This requires that you specify the duration of the simulation. 
 Output Control under MT3DMS, in the Translation settings tree 
The MT3DMS Output Settings will appear. Here you can define the total time of the transport 
simulation. 
 Type: 3650 under Simulation time length 
 Type: 10000 under Max Number of Transport Steps 
Next you will define the different times where you want the simulation results to be saved. 
 button to add an additional row to the grid 
 button 7 additional times to add a total of 8 rows 
Enter the following values in the grid, starting at the first (top) row (values expressed here are in 
days): 
 1 
 30 
 60 
 180 
 365 
 730 
 1825 
 3650 
Your screen should look like the image below: 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
 
You are now ready to create the input files (packages) for MODFLOW and MT3DMS. 
 button located on the workflow toolbar 
Visual MODFLOW Flex will now create the files necessary to run MT3DMS and MODFLOW-2005. You 
will see a progress of the Translation which should take approximately 5-10 seconds. Once complete, 
 [Next Step] proceed to the next step in the workflow 
 button located on the workflow toolbar 
The numeric engines will start running, and display progress in the main window. MODFLOW-2005 
will run first, followed by MT3DMS. This simulation should take a minute or less to complete, 
depending on computer speed. MT3D automatically determines the step size for contaminant 
transport by attempting to minimize numerical dispersion and oscillations as the functions relate to 
flow velocities and grid size of the model. 
In this simulation, the optimal time step determined is less than 30 days. Depending on the 
simulation, the optimal time step may be quite small and result in extremely long run times. 
Extended run times are common when pumping wells develop high flow velocities in the area around 
the well screen. 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
The engines progress window will once again appear. MODFLOW will run as before, followed by 
MT3DMS. As MT3D runs, the transport step, step size, and total elapsed time are displayed. 
The current period and transport step being analyzed is displayed in the progress window. 
Once the simulation is complete, you should see a line entry “Program completed.” in the progress 
window. In addition, you will see a new item “Concentration (Conc001)” appears on the model tree, 
under Outputs / Transport. 
Section 16: Viewing Concentration Simulation Results 
 [Next Step] proceed to the next step in the workflow 
You will be presented with an option to View Results, and select the desired results type 
 View Maps 
The concentration distribution can be visually analyzed in Visual MODFLOW in a variety of ways. One 
option is to contour and customize the concentration distribution. Contouring simulation results 
allows you to produce a range of contour plots for your site-specific results. 
By default, Heads will be displayed in the View Maps step. You will remove Heads from the view, and 
display Concentrations. 
 □ Heads remove the check box beside Heads in the Model Explorer 
  Concentrations (Conc001) add a check box to Conc001 in the Model Explorer 
Examine your simulation results in cross-section. 
 Type: 3 under Layer to display layer 3 
  Row from the list of views 
 Type: 20 under Row, to display row 20 
 to remove gridlines 
You will now see a Layer (plan) view of the plume and a cross sectional view, or slice, through the 
contaminant plume for the first time step (1 day). Adjust the vertical exaggeration as required 
(ensure you have the Row view selected to enable changes to the vertical exaggeration). Your 
interface should look like the image below: 
Note: if your results display a uniform concentration of 0 
mg/L across the entire model domain it is likely that your 
concentration input values were overwritten. If you notice 
abnormallylow concentrations please revisit your boundary 
condition inputs to ensure that concentrations have been 
applied correctly. 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
 
Notice the Observation Well 1 (OW-1) you specified earlier does not appear in the cross- sectional 
view. You can show/hide these objects from the model tree, by adding/removing the check box 
beside the desired data object. The same is true for any raw data you wish to display, such as 
shapefiles, air photos, etc. 
Next, step through the model output time steps to examine the evolution of the contaminant plume. 
Above the Layer and Row views, you will see a toolbar; in the middle, is a combo box, which display 
all the output times you previously defined. 
 to display the Next Time Step 
 
The Layer and Row views should update to reflect the values of concentrations calculated for 30 
days. 
 to display the Last Time Step 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
 
Note: if the toolbar for selecting output times does not 
appear simply deselect/reselect the Concentration output 
object under the Model Explorer. Refreshing the view in this 
way typically resolves any display issues relating to the 
time-step buttons. 
The Layer and Row views should update to reflect the values calculated for 3650 days (alternatively, 
you can select a specified time from the combo box adjacent to the time advancer buttons, to 
proceed directly to the desired time). 
 
Note that like the display of heads values, you can move the mouse around the Layer or Row view, 
and see the calculated values for each cell in the status bar at the bottom of the window. 
Section 17: Displaying a Concentration versus Time Graph 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
Using OW-1, Visual MODFLOW can produce and display a contaminant concentration versus time 
breakthrough graph. This feature is useful for examining the predicted contaminant concentration 
at any point you specify in the model. To display the graph, follow these steps: 
 View Charts from the Workflow tree 
 Transport from the Parameter menu 
 Time Series from the Chart Type menu 
  All Obs. check box under Chart Type 
 Apply at the bottom of the window 
 
This will display a concentration-versus-time graph. Double clicking on any point or any portion of 
the plotted curve will display a pop-up, which will give you the exact data pertinent to that point 
(clicking again will remove it). 
From this graph, the maximum BTEX concentration after approximately 1460 days of transport is 
about 76 mg/L. 
Now is a good time to save the project. 
 File / Save Project from the main menu 
 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
PART 3: DEFINING A REMEDIATION CAPTURE WELL 
The remedial option to be evaluated in this exercise is a single-well pump-and-treat system to 
capture the groundwater plume, preventing further contaminant migration and removing the 
groundwater for treatment. Apart from the contaminant plume that you have calculated in Part 2 of 
this exercise you will utilize backward tracking particles to determine the area of influence, or 
capture zone, for this pumping well operating at a specified rate. You will also determine the optimal 
pumping rate for the single well that maximizes the operational effectiveness of the system by 
capturing and removing the entire groundwater contamination plume. 
Design Objectives 
The design process of a pump-and-treat remediation system focuses on the maximization of both 
the operational effectiveness and the efficiency of the remediation system, while simultaneously 
meeting clean-up targets. 
Visual MODFLOW Flex models can be very powerful tools. Remediation engineers commonly use 
these models during the initial feasibility study stage of remedial alternative selection, and later in 
the design process of groundwater remediation systems. The model enables you to develop an initial 
system design to meet operational goals and clean-up targets. The model also enables you to explore 
cause-and-effect scenarios to assess overall remediation system sensitivity to local geologic and 
hydrologic extremes. 
In this exercise, you will use particles and the calculated contamination plume distribution to 
evaluate the effectiveness of the pump-and-treat remediation system. You will design the system to 
hydrodynamically capture and remove all of the contaminant particles in the groundwater with the 
interceptor well, while trying to minimize the amount of clean water removed for treatment. 
Section 18: Assigning the Pumping Well 
 Define Boundary Conditions from the workflow tree 
 Wells from the list menu under Toolbox 
Before you proceed, make sure you are viewing model Layer 1. You can quickly determine your 
present location in the model by viewing the values for Layer, Column and Row under the Views 
section. 
The well must be imported from an excel file. 
 File / Import Data… a Data Import window will open 
 Well from the data type drodown list 
 […] to browse to the correct file 
A dialogue box opens that allows you to browse for the appropriate file. In the project directory 
(C:\VMODFlex\Intro1\), choose the following file: 
 Pumping_wells.xls 
 Open 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
 Next >> from the Data Import window 
 Next >> in the preview window 
The following window will appear: 
 
In this window you define what well data to import. Under the “Select the type of data you want to 
import” 
  Well heads with the following data 
  Screens 
  Pumping Schedule 
 Next >> from the Data Import window 
 Next >> 
 Next >> fields are mapped automatically 
 Finish 
A new data object, Pumping_wells will appear in the Model Explorer tree. 
 Pumping_wells select from the Data Tree 
 Assign from the Toolbox in the main window 
 Using Data Object from the dropdown menu for Assign 
A new window ‘Create Well Boundary Condition’ will open. 
 in the upper left corner, under Select 
 Raw Wells Data Object 
 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
 
 OK 
The well will now appear in the grid view, located at X=94, Y=86 in layers 3 and 4 – the layers where 
the well is screened. If the well is not visible, please ensure you have zoomed out to view the full 
extents of the model. 
 from the toolbar above the Layer view window 
 Type: 3 under Layer to display layer 3 
Your display should appear as shown below: 
 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
 
A circle will appear indicating the location of the interceptor well. The well is screened over the 
interceptor trench, with a top at 23.6, and a bottom at 18.25 m. 
The screened interval for PW-1 has been restricted to Layer 3 and Layer 4, which are the numerical 
model layers most likely to be exposed to contamination. This approach will help minimize problems 
associated with drying of cells at the pumping well. Specifically, as MODFLOW 2005 attempts to find 
a solution, it will iteratively assign heads at all cells, including the cells representing the pumping 
well. If the head falls below the bottom of a cell that represents part of a screen for the pumping 
well screened over more than 1 layer, the cell is automatically turned off and the pumping rate is 
decreased proportionately. 
The well is pumping at a rate of -60 m3/day for a duration of 3650 days (10 years) 
Note on convention: The pumping rate must be a negative 
value to establish an extraction well. A positive pumping 
rate would indicate an injection well. 
Now is a good time to save the project. 
 File / Save Project from the main menu 
Section 19: Assigning Particles 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
The forward particles that you assigned previously will be re-assigned to the refined grid and to Layer 
2, 3 and 4 to determine if the water flowing through the contaminated area will be captured by the 
pumping well. Another aspect of well design is to minimize the amount of uncontaminated water 
that is being collected. This can be assessed by assigning backward-tracking particles in a circle 
around the well. These particles will help to delineate the capture zone of that well and we will be 
defining them in the screened Layers 3 and 4. If the capture zone is significantly larger than the 
contaminated zone, the design should be modified e.g. lower pumping rate, more wells, etc. 
First, we need to redefine the particles, in the workflow select: 
 Define Particles from the main Workflow menu 
 Assign from the Toolbox 
 Using Data Object… from the pop-up menu 
At this step, you choose the particles points data object, and convert these into particles. 
 particles points data object, from the Data Tree 
 from the Create New Particles window 
  Forward as the Particle Type 
  Layers 2, 3 and 4 to assign particles to additional layers 
The window should appear as follows: 
 
 OK to accept the default settings, and create the particles 
The particles should now appear as points, in the layer view. These are located along column 13 in 
the grid. 
We will now add a circle of backward tracking particles around the well in layers 3 and 4. Change 
the layer to layer 3 
 Type: 3 under Layer to display layer 3 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
You should now be viewing Layer 3. Ensure the pumping well is visible in the model domain. 
 Well1 from the Model Explorer, under Inputs 
 
 Assign from the Toolbox in the main window 
 Circle from the pop-up menu 
 Left-click on the point representing the pumping well 
The following window will appear: 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
 
 Radius: 1.8 to change the radius of deployment 
  Layer 4 to deploy particles in layers 3 and 4 
The window should appear as follows: 
 
 OK to create the particles 
A circle of particles should appear around the well location, colored in maroon red. If you wish, you 
can zoom into this region to check the particle location. Once you are done, be sure to zoom back 
out to full extents (click the Zoom Full Extents button from the toolbar). 
 
Now is a good time to save the project. 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
 File / Save Project from the main menu 
Section 20: Running the Pump-and-Treat Remediation Simulation 
To run a simulation with the new data set, 
 Single Run from the main Workflow menu 
You will be presented with an option to Compose Engines. This dialogue will list the numeric models 
that can be used to simulate groundwater flow, particle tracking, water budgets, contaminant 
transport, and parameter estimation. For this simulation you should select MODFLOW- 2005 and 
MODPATH to be run (as indicated by a  in the box), uncheck MT3DMS. It is generally a good idea 
to run a quick MODFLOW & MODPATH simulation prior to running MT3DMS since this will allow you 
to see if the pumping rate provides suitable capture zone coverage of the plume; in addition, 
MT3DMS simulations can often require much longer run times (typically several hours) as the model 
size, complexity and time length increase. 
 □ Run Transport Engine to deselect MT3DMS 
  MODPATH ensure MODPATH is selected 
 [Next Step] proceed to the next step in the workflow 
The Translate step will appear; there are no changes need for this step, so you are now ready to 
create the input files (packages) for MODFLOW and MODPATH. 
 button located on the workflow toolbar 
Visual MODFLOW Flex will now create the files necessary to run the USGS MODFLOW and MODPATH 
programs. You will see a progress of the Translation, which should take approximately 5-10 seconds. 
Once complete, 
 [Next Step] proceed to the next step in the workflow 
 button located on the workflow toolbar 
MODFLOW-2005 will run first, followed by MODPATH. Each engine will have an information window 
that displays simulation results and progress. Clicking on the tab of the respective window will enable 
you to view detailed results of each run. You will notice two tabs for MODPATH, one representing 
the forward tracking particles and one representing backwards tracking particles. 
The run should take 10-20 seconds. Once the simulation is complete, you should see a summary of 
the results from the MODPATH run in the MODPATH tab. 
Section 21: Displaying the Pump and Treat Simulation Results 
 [Next Step] proceed to the next step in the workflow 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
You will be presented with an option to View Results, and select the desired results type 
 View Maps button from the main window 
To determine if the interceptor well was effective in capturing the plume, you will need to display 
the pathlines. 
 □ Row to view only in plan/layer view 
  Backward Pathlines from the Model Explorer, under Outputs 
  Well 1 from the Model Explorer, under Wells 
A plot of the head equipotentials and particle pathlines will be displayed as shown in the figure 
below. You will see that a pumping rate of 60 m3/d is sufficient to capture the plume fully (as 
indicated by the fact that no pathlines are going beyond the extraction well). 
 
If you wish, you can also experiment with more than one extraction well. Using multiple wells in an 
interception system is generally advisable because it allows the system to continue functioning if one 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
of the pumps breaks down or when the wells require maintenance. In the next section, you will re-
run the simulation but this time including MT3DMS in the calculations. 
Section 22: Running the Pump-and-Treat Remediation Simulation with MT3DMS 
Now let us run MT3DMS to check if the plume is fully captured also for the contaminant transport. 
To run a simulation with the new data set: 
 Single Run option in the Workflow tree 
You will be presented with an option to Compose Engines and the dialogue box will list the numeric 
models. For this simulation you should select MODFLOW 2005, MODPATH and MT3DMS to be run. 
  Run Transport Engine to select MT3DMS 
 [Next Step] proceed to the next step in the workflow 
 button located on the workflow toolbar 
Once complete the translation is completed, 
 [Next Step] proceed to the next step in the workflow 
 button located on the workflow toolbar 
The MT3DMS simulation will be completed once you see a message at the bottom of the run log 
which says ‘***** The run was successful. *****’. 
To visually analyze the modeling results: 
 [Next Step] proceed to the next step in the workflow 
 View Maps button from the main window 
To see if the interceptor well was effective in capturing the contamination plume, you will need to 
display the concentration distribution. 
 □ Heads remove the check box in the Model Explorer Tree 
  Concentration (CONC001) add a check box in the Model Explorer tree 
Examine your simulation results in cross-section. 
  Row from the list of views 
 Type: 17 under Row to display row 17 
A plot of concentration isolines with colors will be displayed. 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
 
 
Now, step thru the model output time steps to examine the evolution of the contaminant plume. 
You can also add the pumping well to this view by selecting this in the Model Explorer 
Above the Layer and Rowviews, you will see a toolbar which controls the output times. 
 to display the Next Time Step 
The Layer and Row views should update to reflect the values of concentrations calculated for 30 
days. To see the concentration distribution after 10 years or 3650 days: 
 to display the Last Time Step 
Your screen display should look like the figure below. 
 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
 
The pumping well seems to be capturing the contaminant plume, indicating that the pumping rate is 
sufficient. However, if you wish to optimise the pumping rate, the model provides a useful tool for 
designing the number of wells, well location and total pumping rate. 
The lesson that we can learn from this simulation is that a full simulation of MODFLOW, MODPATH 
and MT3DMS are necessary to understand the impact of remediation well capture of a contaminated 
plume. 
A color map of the results can also be shown in the 3D viewer. 
  3D from the list of views 
 □ Layer from the list of views 
 □ Row from the list of views 
This view will show three slices through the model (along the selected layer, row, and column). 
Ensure the initial particle locations are active and navigate to layer 3. 
  Forward Pathlines add a checkbox in the Model Explorer Tree 
  Backward Pathlines add a checkbox in the Model Explorer Tree 
  Particles add a checkbox in the Model Explorer Tree 
 Type: 3 under Layer to view layer 3 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
 
 
Now is a good time to save the project. 
 File / Save Project from the main menu 
 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
PART 4: 3D VISUALIZATION AND INTERPRETATION 
Viewing modeling results in three dimensions is often the best way to gain insight into the flow and 
transport characteristics of a site. For example, you may wish to create: 
• Arbitrary horizontal slices through a model domain; 
• Vertical cross-sections along or perpendicular to a flowline; 
• Vertical cross-sections through a set of receptors, such as drinking-water wells; 
• Three-dimensional isosurfaces that represent migrating contaminant plumes. 
These types of views allow the hydrogeologist to examine the results in a way that is most relevant 
to the purpose of the analysis. Furthermore, two and three-dimensional animation techniques can 
be useful for illustrating time-dependent processes such as contaminant transport or water table 
drawdown. This section of the exercise will familiarize you with some techniques for assessing your 
transport modeling results in three dimensions using the 3D Explorer. 
Section 23: View 3D Contaminant Plume as an Isosurface 
Next, you will create a 3D volumetric representation of the contaminant plume within the model 
domain by creating an isosurface for a selected concentration value. A value of 10 mg/l will be used 
as it represents the maximum allowed concentration for the local water quality guidelines. The 
isosurface will encapsulate (and draw) any grid cells that have a concentration value greater than or 
equal to 10 mg/l. 
 Window / New 3D Window from the main menu 
A 3D visualization window will open in a new tab. Activate elements of your model by using the check 
boxes in the Model Explorer and Data Tree. 
  Concentration(Conc001) from the Model Explorer, under Outputs 
The 3D grid of the MT3DMS results will appear, with all cells drawn. 
 Right-click on Concentration(Conc001) from the Model Explorer, under 
 Outputs 
 Settings from the menu that appears 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
 
The Settings dialog will appear. Next you will turn off the Cells view and turn on the desired color 
map and Isolines. 
 + Style from the settings tree on the left 
 Cells from the settings tree on the left 
 □ Show Cells uncheck box from the top of the settings window 
 Isosurfaces from the settings tree on the left 
  Show Isosurfaces check box from top of the settings window 
 Add click this button 
This will produce the Isosurface properties dialogue window, which allows you to specify the 
concentration value and visual attributes for the isosurface. 
 Type: 10 in the Attribute Value field 
  Visible check box to activate the isosurface 
  Show Border check box to activate border 
Once completed, your dialogue window should appear as seen below: 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
 
 OK to close the window 
 Apply tp update the 3D View with new settings 
Your screen should now display an isosurface for BTEX equal to 10 mg/L. (you may need to move the 
settings window to the side to see the main VMOD Flex window in the background) 
 + Time from the settings tree on the left 
 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
You can see that the default output time that is selected is the end of the simulation (3650 days). To 
show the time label on the 3d view, 
  Show Time Label check box to include time label 
 Select time = 3650 days to display output results at final time step 
 Apply to update the 3D View with new settings 
 OK to close the window 
Your display should now appear similar to the figure on the following page, as the contaminant 
plume (isosurface) now displays at 10 mg/L after 3650 days. 
 
You may need to adjust the 3D Viewer zoom and rotation in order to get a better perspective of the 
3D groundwater model. 
 Left-click near the bottom of the 3D Viewer window. While 
 holding down the button drag the mouse toward 
 the top of the screen, then release the button 
 Zoom out using the button on the 3D viewer toolbar, or by 
 scrolling down on your mouse cursor wheel 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
 
If you wish, you can view the isosurface for other time steps by using the same procedure as outlined 
above. 
Section 24: Viewing Input Data 
The Visual MODFLOW Flex 3D Viewer also allows you to display the model input data in this 3D 
perspective. Select different model objects from the Data tree and the Model Explorer tree to view 
these in 3D. Add checkmarks to the objects you wish to view. You may adjust the exaggeration of 
the viewer at the bottom of the viewer window. 
The settings of the model objects can also be modified individually to user specification. Please spend 
time to familiarize yourself with these options. Your viewer window may appear similar to the one 
below when you are finished. (in this example, the following data objects are set to visible: 
• basemap and Pumping_wells (from the data panel) 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
 
 
• Constant Head 1 and Constant Head 2 (from Model Explorer in the model Inputs) 
• Forward Pathlines and Backward Pathlines (from Model Explorer in the model Outputs) 
 
Section 25: Defining Colormap with Isolines 
The Visual MODFLOW Flex 3D Viewer allows you to plot colormaps and contour maps of selected 
model properties on any horizontal, vertical, or cross-sectional surface through the model domain. 
Let’s add a colormap of the calculated head values in the model domain. 
  Heads from the Model Explorer tree, under Outputs 
The 3D grid of the Heads results will appear, with all cells drawn. 
 Right-click on Heads from the Model Explorer tree 
 Settings from the menu that appears 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
 
 
 
 + Style from the settings tree on the left 
 Cells from the settings tree on the left 
 □ Show Cells uncheck box from the top of the settings window 
 Colormap from the settings tree on the left 
  Show Colormapcheck box from top of the settings window 
 Type: 10 as the row number 
 Apply to apply changes and add the colormap 
We will make a few additional changes before closing the settings window. 
 + Isolines from the settings tree on the left 
  Show Isolines check box from the top of the settings window 
 Slice Type to expand this combo box 
 Layer from the list of slice types 
 Type: 3 for the Layer Number 
Next you will adjust the contour interval from the settings at the bottom half of the window 
  Contour Interval select radio button 
 Type: 0.25 for the Contour Interval 
The settings should now appear as shown below. 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
 
 Apply to apply changes and add the contour intervals 
 OK 
The 3D Display should now appear as shown below. 
Note: your display may appear differently, depending on the 
rotation or zoom level you have set). Use the rotate and pan 
options to adjust the view as desired. 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
 
3D view is zoomed in view with Exaggeration = 5 
You may also export this view to an image file. 
 Right-click in the 3D Viewer window 
 Save As Image from the pop-up menu 
 […] beside the File Name field 
Browse to the project location (default is C:\Users\<username>\Documents\Visual MODFLOW 
Flex\Projects\Intro1) 
 Type: 3D Image as the File Name 
 Save 
 OK to save the image 
The image will be saved as a bitmap for further use in reports, documentation, etc. 
 
 
***** This concludes the Intro exercise ***** 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
 
References 
Borden, R.C., et al., 1997. Anaerobic Biodegradation of BTEX in Aquifer Material, Environmental 
Research Brief, US Environmental Protection Agency, EPA/600/S-97/003 (copy included in course 
notes) 
Clement, T.P., C.D., Johnson, Y. Sun, G.M. Klecka, C. Bartlett, Natural attenuation of chlorinated 
solvent compounds: Model development and field-scale application, vol.42, p.113-140, Journal 
of Contaminant Hydrology, 2000. 
Clement, T.P., Y. Sun, B.S. Hooker, and J.N. Petersen, 1998. Modeling multi-species reactive 
transport in groundwater aquifers, Groundwater Monitoring & Remediation Journal, vol 18(2), 
spring issue, p. 79-92. 
Johnson, C.D., R.S. Skeen, D.P. Leigh, T.P. Clement, and Y. Sun, 1998. Modeling natural attenuation 
of chlorinated ethenes at a Navy site using the RT3D code, Proceedings of WESTEC 98 conference, 
sponsored by Water Environmental Federation, Orlando, Florida, October 3-7th. 
Guoping & Clement, Prabhakar & Zheng, Chunmiao & Wiedemeier, Todd. (1999). Natural 
Attenuation of BTEX Compounds: Model Development and Field‐Scale Application. Ground 
water. 37. 707-17. 10.1111/j.1745-6584.1999.tb01163.x. 
McDonald, M.G., and A. W. Harbaugh, 1988. A modular three-dimensional finite- difference flow 
model, Techniques in Water Resources Investigations of the U.S. Geological Survey, Book 6., 586 
pp. 
Sun, Y. and T.P. Clement, 1998. A decomposition method for solving coupled multi- species 
reactive transport problems. Transport in Porous Media Journal, 1404, p. 1-20. 
Wiedemeier, T.H., et al., 1995. Technical protocol for implementing intrinsic remediation with 
long-term monitoring for natural attenuation of fuel contamination dissolved in groundwater, 
Volume 1 & 2, Air Force Center for Environmental Excellence, Technology Transfer Division, 
Brooks AFB, San Antonio, Texas. 
Zheng, C., 1990. A modular three-dimensional transport model for simulation of advection, 
dispersion and chemical reactions of contaminants in groundwater systems, 
U.S.E.P.A. Report. 
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Visual MODFLOW Flex Exercise: 3D Capture 
 
 
Visual MODFLOW Flex Exercise – 3D Capture 
3D Pathline and Capture Zone Analysis 
Exercise Objectives 
• Develop a Visual MODFLOW Flex model using a georeferenced Bitmap (BMP) as a basemap 
• Evaluate effects of vertical anisotropy and recharge on 3D containment volumes and 
capture zones for wells in multi-aquifer systems 
• Perform particle tracking, and evaluate two-dimensional versus three-dimensional capture 
zones 
• Determine effect of all no-flux boundary conditions on steady-state simulations 
Problem Description 
In capture zone and containment volume analysis for groundwater clean-up, the presentation by 
Larson et al. (1987) is one of the first attempts to illustrate the significant differences between 
three-dimensional and two-dimensional model results of capture zones and containment volumes. 
Until that time, and even today, most aquifers were analyzed with two-dimensional models, the 
majority isotropic in nature. 
These authors point out how: 
• Horizontal area of the containment volume at the water table (for a pumping well) is 
determined by the rate of recharge [Area = Pumping rate/Recharge]; and, 
• Shape of the containment volume below the water table is determined by the degree of 
partial penetration, the horizontal to vertical hydraulic conductivity ratio, the rate and 
direction of groundwater flow and any present heterogeneities. 
These generalities are valid provided recharge is the major source of water (surface water sources 
are negligible). For example, homogeneous, anisotropic aquifers show that deeper penetration of 
the pumping well and/or a higher vertical hydraulic conductivity will increase the depth of 
containment and decrease the width. The opposite is true for shallow penetrating wells and low 
vertical hydraulic conductivities. 
Several examples illustrating these concepts are presented including a three-dimensional, 
contaminant capture zone problem for an anisotropic [Kh/Kv], multi-aquifer system with recharge. 
In this example, which models the capture of a contaminant plume, despite a well-placed fully 
penetrating well at the head of the plume, the resulting three-dimensional containment volume 
showed most of the plume was not captured. Although not widely cited in the literature, their 
work is very instructive for the implications it has for contaminant plume capture designs and 
wellhead protection analyses in heterogeneous, anisotropic, three-dimensional aquifers in which 
recharge plays a significant role. 
The dotted line in the upper figure of Figure 1 (below) shows the shape of the contaminated 
containment volume for the middle of the sand layer, predicted by a two-dimensional model that 
did not account for vertical flow. The lower figure in Figure 1 shows a vertical profile of the true 
containment zone, using a three-dimensional model that did account for vertical flow. If this clean-
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Visual MODFLOW Flex Exercise: 3D Capture 
 
 
up design had been based on a two-dimensional model, it would fail since most of the "expected" 
containment volume would not be captured. Indeed, in the case of a two-dimensional design, a 
plot of concentration vs. time would show a decrease until zero was reached, at which point one 
might erroneously conclude there is no more contamination and the operation was a success. 
 
Figure 1 - Simulated 3D Containment Volume for Multi-Aquifer System 
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Visual MODFLOW Flex Exercise: 3D Capture 
 
 
These results were obtained using the USGS's Trescott and Larson (1976) three-dimensional flow 
model together with a simple pathline model. The use of the USGS's MODFLOW and MODPATH 
for the same problem results in very similar, but not equal, results. Let's use Visual MODFLOW Flex 
(and the USGS MODFLOW-2005 and MODPATH programs) to simulate this problem. 
References 
Larson, S.P., C.B. Andrews, M.D. Howland and D.T. Feinstein (1987). Three-Dimensional Modeling 
Analysis of Ground Water Pumping Schemes for Containment of Shallow Ground Water 
Contamination. Proceedings of the Conference on Solving Ground WaterProblems with Models, 
Volumes 1 & 2, Denver, CO. National Ground Water Association, Dublin, OH. pp. 517-530 
US EPA, 2002. Elements for Effective Management of Operating Pump and Treat Systems. EPA 
report 542-R-02-009, OSWER 9355.4-27FS. Can be downloaded at http://clu-
in.org/techpubs.htm 
US Army Corps of Eng., 2000. Operation and Maintenance of Extraction and Injection Wells at 
HTRW Sites. Engineers Pamphlet EP 1110-1-27. Can be downloaded at: 
http://www.usace.army.mil 
US EPA, 2008. A Systematic Approach for Evaluation of Capture Zones at Pump and Treat Systems. 
EPA Report 600/R-08/003, Office of Research and Development, National Risk Management 
Research Laboratory, Ada, OK. 
Terms and Notations 
For the purposes of this tutorial, the following terms and notations will be used. (This assumes you 
are using a right-handed mouse.) 
type - type in the given word or value 
↔ - press the <Tab> key 
 - press the <Enter> key 
 - click the left mouse button where indicated 
 - double-click the left mouse button where indicated 
Starting Visual MODFLOW Flex 
On your Windows desktop, you will see an icon for Visual MODFLOW Flex 
 Visual MODFLOW Flex to start the program. 
The following Visual MODFLOW Flex window will appear: 
http://www.usace.army.mil/
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Visual MODFLOW Flex Exercise: 3D Capture 
 
 
 
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Visual MODFLOW Flex Exercise: 3D Capture 
 
 
PART 1: CREATING A PROJECT AND GENERATING A GRID 
The first step to groundwater modeling with Visual MODFLOW Flex is to create your project and 
generate a grid. 
Section 1.1: Create Project 
To create a new project: 
 File / New Project… from the top menu bar 
A Create Project dialog box will be displayed prompting you to enter the project name of the new 
Visual MODFLOW Flex project. 
 
 Type: 3DCapture as the project name 
 Browse button under Data Repository 
 Select a directory on the hard drive (or use the default location) 
Note: By default, new Visual MODFLOW Flex projects will 
be saved to the following location - 
[C:\Users\<username>\Documents\Visual MODFLOW 
Flex\Projects] 
Ensure that the correct system of units has been specified. Select the following units: 
 Length: ft 
 Time: day 
 Conductivity: ft/d 
 Pumping Rate: GPM 
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Visual MODFLOW Flex Exercise: 3D Capture 
 
 
 Recharge: in/year 
 Specific Storage: 1/ft 
 Mass: kg (irrelevant – no transport simulation) 
 Concentration: mg/L (irrelevant – no transport simulation) 
All other values can remain at their default settings. 
 OK button in the lower right corner of this window. 
The following window will then appear: 
 
The Select Modeling Scenario allows you to choose whether to proceed with the Conceptual or 
Numerical modeling workflow. The conceptual modeling workflow allows you to import all data 
objects into Visual MODFLOW Flex and to build a conceptual site model (CSM). The CSM can then be 
used as a starting point for several different numerical models. In other words, numerical model (i.e. 
with different grid types, engines, etc.) can be quickly and easily created based on the same 
conceptual modeling. This makes it easy for the user to manage several different numerical models 
with slight variations. 
Conceptual modeling is not covered in this exercise, so we will proceed with the numerical modeling 
workflow: 
 Numerical Modeling 
Proceeding with the numerical modeling workflow will bring you to the first step in the that 
workflow, which is to define your model objectives. This step allows you to specify whether you will 
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Visual MODFLOW Flex Exercise: 3D Capture 
 
 
be running a fully saturated or variably saturated model, whether contaminant transport will be 
included, which flow/transport engines will be utilized, etc. You will see the following window open, 
which displays the Define Modeling Objectives step in the numerical modeling workflow: 
 
The Define Modeling Objectives step allows you to specify what kind of model will be run (i.e. flow 
type, whether contaminant transport will be considered, etc.) and to specify some default project 
settings (i.e. default conductivity, storage values, etc.). 
For this exercise, the Start Date can be left at the default setting (i.e. today’s date). However, if time-
stamped data are to be imported from outside sources, then it is necessary to have the start date 
fall at or prior to the oldest data point. 
We will retain most of the default settings in this step, but we will provide new values for the Default 
Project Property Settings: 
 Type: 8.8 for Kx 
 Type: 8.8 for Ky 
 Type: 0.0628 for Kz 
 Type: 0.001 for Ss 
 Type: 0.27 for Sy 
We will leave the remaining default flow parameter values as they were: 
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Visual MODFLOW Flex Exercise: 3D Capture 
 
 
 [Next Step] proceed to the next step in the workflow 
 Yes to dismiss the warning regarding model 
 start date 
Section 1.2: Define Model Grid 
The Define Grid window will appear, allowing you to select whether to import an existing grid or 
create a new one. We will create a new grid in this exercise: 
 Create Grid 
This will bring you to the Create Grid step in the numerical modeling workflow. At this step you will 
specify the boundary/extents of your model and the structure of your model’s grid. Your screen 
should look like the image below: 
 
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Visual MODFLOW Flex Exercise: 3D Capture 
 
 
Now you will specify the number of rows, columns, and layers to be used in the model. Under the 
Grid Definitions frame, enter the following model rows, columns, layers and depth information in 
the appropriate boxes: 
 Rotation = 275 
 Rows = 21 
 Columns = 30 
 Xmin = 15000 
 Xmax = 21000 
 Cell height = calculated this value can be adjusted as per project requirements 
 Ymin = 45000 
 Ymax = 48000 
 Cell width = calculated this value can be adjusted as per project requirements 
For this exercise, you will ignore the option “Calculate extents from a polygon object”. Next, specify 
the parameters for the vertical grid discretization: 
 Type: 10 For the Number of Layers 
Specify the layer elevations (typing the values directly into the grid): 
Layer Name Elevation 
Layer1 - Top: 280 
Layer2 - Top: 220 
Layer3 - Top: 205 
Layer4 - Top: 190 
Layer5 - Top: 180 
Layer6 - Top: 165 
Layer7 - Top: 150 
Layer8 - Top: 142.5 
Layer9 - Top: 135 
Layer10 - Top: 80 
Layer10 - Bott: 20 
The screen should now look like the image below: 
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Visual MODFLOW Flex Exercise: 3D Capture 
 
 
 
 Create Grid Click the ‘Create Grid’ button at the top-right 
 [Next Step] proceed to the next step in the workflow 
Visual MODFLOW Flex will then construct a 30 columns x 21 rows x 10 layers finite difference grid 
with uniform grid spacing in both the X and Y directions, and will automatically create the model run 
Input tree structure. By default, you will be taken to the View/Edit Grid step as shown in the 
following image: 
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Visual MODFLOW Flex Exercise: 3D Capture 
 
 
 
The ‘View/Edit Grid’ portion of the workflow allows the user to make any necessary changes to the 
grid structure. This is particularly useful if you are following the conceptual modeling workflow and 
would like to test slight variations in the grid structure. Let’s load a site map to ensure that the model 
extents match-up with our desired model boundary. 
Section 1.3: Add Basemap 
You will select a bitmap file (.BMP) to be used as a background base map for your model. 
 File / Import Data… from the main menu 
 Select ‘Map’ in the ‘Data Type’ list menu 
 […] button next to ‘Source File’, to browse to 
 the data import file 
 Browse to the location where you downloadedthe 
 ‘Supporting Files’ folder 
 ‘Mayberry.dxf’ in your project directory 
 Open to open the data file 
 Next >> to accept default settings 
 Next >> to accept default settings 
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A Data Import window will open, which allows you to georeferenced the imported map object. The 
Data Import window should look like the image below: 
 
The center of the Data Import window displays the imported map object. The frame on the right 
displays georeferenced information used for the import. As you can see in the imported image, the 
map already displays two points on the map with their local coordinates. We will use these two 
points to georeferenced this site map. First, we will add two georeference points, then we will 
provide coordinates to the points, and finally we will perform a georeference ‘transformation’ to the 
map object. The transformation will reorienting/resizing the image to align with our project 
coordinates. 
 click Zoom tool 
 Click and drag to select the area around the 
 georeferenced point in the bottom left 
 (13240, 45443) 
 to add a new georeference point 
 Click in the center of the cross which indicates the exact location of the 
georeference point 
A new Coordinate for Control Point window will open, as shown below: 
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Visual MODFLOW Flex Exercise: 3D Capture 
 
 
 
 Type: 13420 in the X field 
 Type: 45443 in the Y field 
 OK 
 to extend the view to the full extent of the 
 image 
 click Zoom tool 
 Click and drag to select the area around the 
 georeferenced point in the upper right 
 (19465, 41783) 
 to add a new georeference point 
 Click in the center of the cross which indicates the exact location of the 
georeference point 
 Type: 19465 in the X field 
 Type: 41783 in the Y field 
 OK 
 to extend the view to the full extent of the 
 image 
The Data Import window should now look like the following image: 
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Visual MODFLOW Flex Exercise: 3D Capture 
 
 
 
You will now perform the georeferencing transformation and finalize the import 
procedure: 
 click Transform button 
 Next >> to proceed to the next step 
 Review the final transformation (notice that the image has been rotated) 
 Finish 
Advance to the View/Edit Grid workflow step. Now activate the basemap by clicking the 
Mayberry object in the Data Explorer. Your display should look like the image below: 
 [Next Step] proceed to the next step in the workflow 
  Mayberry activate this object in the current view by 
 clicking in the Data Tree 
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Visual MODFLOW Flex Exercise: 3D Capture 
 
 
 
As you can see, the finite difference grid is not quite in line with the site map. The 
reason for this discrepancy is that the grid origin point is shifted whenever a grid 
rotation is applied, in order to preserve the overall grid extents. To reorient the grid, we 
will click the ‘Edit Grid’ button and alter the Define Grid script which is used during the 
translation step. 
 Edit grid… click button under the Toolbox 
 Script click tab at top of Edit Grid window 
 Type: dx = 15000 in the ‘Shift grid origin by’ line 
 Type: dy = 45000 in the ‘Shift grid origin by’ line 
 OK to accept changes edit grid 
Performing this grid edit will once again generate a new finite difference grid and the 
associated file structure within the Model Explorer. A new tab and numeric modeling 
workflow window (named NumericGrid1_refined-Run1) will open. Reactivate the map 
object and your display should look like the image below: 
  Mayberry activate this object in the current view by 
 clicking in the Data Tree (it may be difficult 
 to see) 
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Visual MODFLOW Flex Exercise: 3D Capture 
 
 
 
Before we proceed any further with this model let’s review the structure of the finite 
difference grid we’ve just created. 
  Row from the list of available views 
 Exaggeration: 1 minimize vertical exaggeration in row view 
 select Zoom to Box tool 
 Click and drag around the area of the visible row 
  Column from the list of available views 
 Exaggeration: 1 minimize vertical exaggeration in column 
 view 
 select Zoom to Box tool 
 Click and drag around the area of the visible column 
Your display will look something like the image below: 
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Visual MODFLOW Flex Exercise: 3D Capture 
 
 
 
Please note that layer 1 represents the surficial silt layer, layers 2-8 represent the upper aquifer, 
layer 9 represents the silt, clay & sand layer, and layer 10 represents the lower sandstone aquifer 
(refer to the image on page 2 of this exercise). We will now proceed to the next step in the workflow, 
which is to define flow properties for the various layers/property zones in this model. 
 
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Visual MODFLOW Flex Exercise: 3D Capture 
 
 
PART 2: DEFINE PROPERTIES AND BOUNDARY CONDITIONS 
Section 2.1: Define Properties 
 [Next Step] proceed to the next step in the workflow 
You will arrive at the Define Properties step in the numerical modeling workflow. Under the 
‘Toolbox’ in the main working window, ensure that conductivity has been selected from the first 
dropdown menu. 
 Conductivity from the list menu under the Toolbox 
 Edit option under the Toolbox 
The default property values will be displayed in the Conductivity dialogue box (image below). As you 
can see, we currently only have a single property zone which covers the entire model area, and the 
default flow properties set during the Define Modeling Objectives step has been applied to the 
entire model. We will add new property zones on a layer-wide basis. 
 
 OK to dismiss the Edit property window 
 □ Row to deactivate, from the list of available 
 views 
 □ Column to deactivate, from the list of available 
 views 
 Conductivity from the list menu under the Toolbox 
 Assign option under the Toolbox 
 Entire Layer/Row/Column from the menu that appears 
The New Property Zone window will open, as shown below: 
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Visual MODFLOW Flex Exercise: 3D Capture 
 
 
 
We will add three new property zones, based on the delineation of layers discussed above (i.e. layers 
2-8 represent the upper aquifer, layer 9 represents the sand/clay/silt layer, and layer 10 represents 
the lower sandstone aquifer). 
 New in the upper left corner of the New Property 
 Zone window, this will create a new property zone 
 Type: 41 under the Value column, for Kx 
 Type: 41 under the Value column, for Ky 
 Type: 0.0171 under the Value column, for Kz 
  Assign to Layers to assign the values to the specified layers 
 □ Layer 1 to deactivate layer 1 
  Layers 2-8 check boxes to apply changes to layers 2-8 
 OK to accept and apply changes 
Repeat this procedure for layers 9 and 10, applying the Kx, Ky and Kz values listed below to the 
appropriate layers. 
 Layer 9 Layer 10 
Kx 26 50 
Ky 26 50 
Kz 0.0108 50 
At this time, you may deactivate the Layer view and activate either the Row or Column view (with a 
vertical exaggeration of 0) to review the new property zone distribution. Your display should look 
like the image below: 
  Row from the list of available views 
 □ Layer to deactivate the layer view 
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Visual MODFLOW Flex Exercise: 3D Capture 
 
 
 Type: 1 in the Exaggeration box 
 select Zoom to Box tool 
 Click and drag around the area of the visible row 
 
Finally, we will double-check the storage flow properties to ensure that we’re happy with those 
values. Since there is only one property zone for storage the default values should be applied to 
every cell in the model. 
 Storage from thelist menu under the Toolbox 
 Edit… option under the Toolbox 
Ensure that the storage property values in your model match the values in the image below (you will 
have to update the Effective Porosity (Ep) value [use F2 or the button to apply values to an entire 
row]): 
 Ep = 0.2 under the Ep column (all rows) 
 (or F2) to assign this value to the entire column 
 
 
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Visual MODFLOW Flex Exercise: 3D Capture 
 
 
 
These material properties are assigned to all the cells in every layer. In this example, we will only be 
dealing with steady-state flow problems. For this reason, we will not be using the storage properties 
of each hydrostratographic unit. Therefore, we can let the storage values (Ss, Sy) for all the lower 
layers be the same as the default values for the upper silt layer. If, however, one would like to 
perform a transient flow analysis in the future, the appropriate storage parameter values must be 
defined for each layer. 
Ep is the effective porosity for flow (nef). It is used to calculate the true groundwater velocity [e.g., 
Vx = Kx/nef (H/X)] that is used in MODPATH to calculate travel times (time markers) along pathlines 
and is used to determine time-related capture zones. We see then that time-related calculations are 
still performed even though the flow field itself may be steady state and not a function of time. 
Now is a good time to save the project: 
 File/Save Project from the main menu 
Section 2.2: Define Recharge Boundary 
We will now apply boundary conditions to our model domain, starting with recharge. We will 
proceed to the next step in the numerical modeling workflow: 
 [Next Step] proceed to the next step in the workflow 
You will arrive at the Define Boundary Conditions step in the numerical modeling workflow. Since 
recharge boundaries may only be applied to the first layer of the model, so will return to the layer 
view and ensure that layer 1 is being viewed: 
  Layer from the list of available views (ensure layer 1 is 
 selected) 
 
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Visual MODFLOW Flex Exercise: 3D Capture 
 
 
 □ Row to deactivate, from the list of available 
 views 
Under the ‘Toolbox’ in the main working window, ensure that Recharge has been selected from the 
first dropdown menu. 
 Recharge from the list of available boundary conditions under 
 the Toolbox 
 Assign option under the Toolbox 
 Entire Layer from the menu that appears 
This will open the Define Boundary Condition window, as shown below: 
 
 Next >> to accept default name (‘Recharge’) 
 Type: 15 under the Recharge (in/yr) column 
 (or F2) to assign this value to the entire column 
 Type: 0 under the Ponding (ft) column (ponding 
 value is only used when MODFLOW-
 SURFACT engines are used, but a value 
 must be entered) 
 (or F2) to assign this value to the entire column 
Please note that by default, recharge boundary conditions are listed with a transient schedule. For 
steady state flow models, the recharge value for the first stress period will be applied to the entire 
duration of a steady state run. Providing a transient recharge schedule is more important when 
preparing a transient model run. 
The Define Boundary Condition window should look like the image below: 
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Visual MODFLOW Flex Exercise: 3D Capture 
 
 
 
 Finish to apply the recharge boundary condition 
A series of white dots have been populated into the Layer 1 cells. You should see the following in 
your display: 
 
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Visual MODFLOW Flex Exercise: 3D Capture 
 
 
 
Section 2.3: Define Pumping Well Boundary Condition 
We will now apply a pumping well boundary condition to the model. Ensure that you are still on the 
Define Boundary Condition step in the workflow, select Wells from the list of available boundary 
conditions, and assign the well manually: 
 Wells from the list of available boundary conditions under 
 the Toolbox 
 Assign option under the Toolbox 
 Wells from the menu that appears 
 Click on the cell at Row 11, Column 26 (see image below) 
 
 Finish from the Toolbox 
The Create Well Boundary Condition window will open. Enter the following information: 
 Type: 220 under Top Elev. (ft) in the Screens table 
 Type: 135 under Bott. Elev. (ft) in the Screens table 
 Type: 3650 under End Time (days) in the Pumping Schedule table 
 Type: -28 under Rate (GPM) in the Pumping Schedule table 
Note: a negative pumping rate indicates that this is an 
extraction well. For injection wells enter a positive 
pumping rate. 
The Create Well Boundary Condition window should look like the image below: 
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Visual MODFLOW Flex Exercise: 3D Capture 
 
 
 
 OK to accept values and apply the pumping well boundary 
 condition 
Please note that Visual MODFLOW Flex will automatically apply the well boundary condition to the 
correct layers, based on the screen depth input during the well creation process. Since the current 
viewer should display layer 1, you will not immediately see the new pumping well. In order to see 
this pumping well please click through layers 2-8. The pumping well will appear as a light-brown dot 
in the appropriate cell. 
Now is a good time to save the project: 
 File/Save Project from the main menu 
 
 
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Visual MODFLOW Flex Exercise: 3D Capture 
 
 
PART 3: REFINE GRID AROUND PUMPING WELL 
We will now apply a grid refinement in the area surrounding the pumping well. The cell which 
contains the pumping well is exactly 200ft wide and 142.88ft long. This means that the well is 
currently calculated to have an effective area of approximately 28,500 ft2. This illustrates one reason 
why grid refinement is often done around well objects. 
We will perform a x3 grid refinement on the row/column containing the actual pumping well, and a 
x2 refinement on the rows/columns surrounding the pumping well (2 rows/columns in each 
direction). 
To perform a grid refinement, we will return to the View/Edit Grid step in the workflow. 
 View/Edit Grid select this step directly from the workflow navigator 
 Edit grid… select this option from the Toolbox 
The Edit grid window will open, as shown below: 
 
This window allows you to select a range of rows/columns and to specify how much the row/column 
will be defined. We’ll run through this process several times. 
  Edit rows ensure you are editing rows 
 Type: 11 under the From field 
 Type: 11 under the To field 
 Type: 3 under the row(s) with field 
 Apply grid edit to apply the current edit 
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Visual MODFLOW Flex Exercise: 3D Capture 
 
 
The Edit grid window should now look like the image below: 
 
Please note that rows 10, 11, 13 and 14 are all highlighted pink now. This is because these rows 
exceed the maximum with ratio threshold of 1.5. 
Large differences in the dimensions of adjacent cells may result in numerical instability and/or 
convergence issues with your model. So we will apply further refinements to ensure that our grid 
will not cause any problems when we run the model. 
  Edit rows ensure you are editing rows 
 Type: 9 under the From field 
 Type: 10 under the To field 
 Type: 2 under the row(s) with field 
 Apply grid edit to apply the current edit 
  Edit rows ensure you are editing rows 
 Type: 16 under the From field 
 Type: 17 under the To field 
 Type: 2 under the row(s) with field 
 Apply grid edit to apply the current edit 
Unfortunately, these rows will continue to exceed the maximum ratio threshold unless we continue 
to refine the entire model domain. This is not desirable, so we will simply proceed with a column 
refinement. 
  Edit columns ensure you are editing columns 
 Type: 26 under the From field 
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Visual MODFLOW Flex Exercise: 3D Capture 
 
 
 Type: 26 under the To field 
 Type: 3 under the column(s) with field 
 Apply grid edit to apply the current edit 
  Edit columns ensure you are editing columns 
 Type: 24 under the From field 
 Type: 25 under the To field 
 Type: 2 under the column(s) with field 
 Apply grid edit to apply the current edit 
  Edit columns ensure you are editing columns 
 Type: 31 under the From field 
 Type: 32 under the To field 
 Type: 2 under the column(s) with field 
 Apply grid edit to apply the current edit 
The final Edit grid window should look like the image below: 
 
 OK to accept changes and exit the Edit grid window 
Performing this grid edit will once again generate a new finite difference grid and the associated file 
structure within the Model Explorer. A new tab and numeric modeling workflow window (named 
NumericGrid1_refined_refined-Run1) will open. 
Now is a good time to save the project: 
 File/Save Project from the main menu 
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Visual MODFLOW Flex Exercise: 3D Capture 
 
 
PART 4: ADDING PARTICLES 
To help define and visualize the containment volume and capture zones, backward tracking particles 
will be placed around the screened portion of the well and a line of forward tracking particles will be 
placed in Layer 1 on both sides of the well (i.e. in Row 14). You should currently be looking at the 
View/Edit Grid step in the workflow. We’ll proceed to the ‘Select the Next Step’ workflow step: 
 [Next Step] proceed to the next step in the workflow 
 [Next Step] proceed to the next step in the workflow 
 [Next Step] proceed to the next step in the workflow 
 Define Particles 
Particles can be assigned using one of three methods: placed manually (cell-by-cell), using a 
preexisting data object, or by placing a circle of particles around an object. Placing a circle of 
backward tracking particles around the well will be simple. For the forward tracking particles we will 
simply assign them manually by selecting the cells where we would like to place a particle. 
To add the forward particles to the same row, it is easier to assign them in cross sectional view. 
  Layer from the list of available views 
 Adjust the view so that you can see all of Row 14 as large as possible 
We will manually place the particles in a straight line within Layer 1, Column 14. Ensure that a particle 
is placed within each cell. 
 Assign button in the Toolbox 
 Point… from the list menu that appears under the Toolbox 
 Click every cell in Column 14 
 Finish button in the Toolbox 
A Create New Particles window will open, as shown below. This window allows you to select whether 
the particles will be forward or backward tracking particles, and to determine which layer the current 
particles will be placed in. 
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Visual MODFLOW Flex Exercise: 3D Capture 
 
 
 
We will leave the Assign to Layer values as they are, since we want to place these forward tracking 
particles in the first layer. However, we do need to specify that these will be forward tracking 
particles. 
  Forward under the Particle Type frame 
 OK to accept remaining options and place the particles 
Note: particle release time is specified during the Translate 
step of the modeling workflow. 
A green circle indicates that the particles have been placed correctly. We will now place a circle of 
backward tracking particles around the pumping well. We’ll place a circle of particles in each layer 
where the pumping well is active (i.e. Layers 2-8). 
  Layer: 2 from the list of available views (Layer 2) 
  Wells activate this object in the Model Explorer, this will 
 make the pumping well visible in the Layer view 
 Assign button in the Toolbox 
 Circle… from the list menu that appears under the Toolbox 
 Click the pumping well 
Once again, the Create New Particles window will open. We will leave the default values here, but 
we will assign these particles to additional layers. Ensure layers 2-8 are selected, backward particles 
are specified as the particle type, with a release radius of 10 ft and 10 particles. The Create New 
Particles window should look like the image below: 
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Visual MODFLOW Flex Exercise: 3D Capture 
 
 
 
 OK to accept remaining options and place the particles 
Now is a good time to save the project. 
 File/Save Project from the main menu 
 
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Visual MODFLOW Flex Exercise: 3D Capture 
 
 
PART 5: RUNNING MODFLOW AND MODPATH 
We have not explicitly set any boundary conditions. If boundary conditions are not specified in 
Visual MODFLOW, by default no-flux conditions are assumed on all boundaries. The only source of 
water for this aquifer system is recharge, while the only discharge of water is the extraction well. 
For the moment, let's see what happens if we use no-flux conditions on all the boundaries and run 
the model under steady state conditions. 
 [Next Step] proceed to the next step in the workflow 
You will be presented with an option to Select Run Type 
 Single Run 
You will be prompted to select which engines to run. By default, MODFLOW-2005 should already be 
selected; you also need to include MODPATH in the model run: 
  MODPATH from the list of available engines 
 [Next Step] proceed to the next step in the workflow 
The translation settings will appear; this allows you to adjust solvers and their parameters (number 
of iterations, head-change criterion, damping factors), package settings, output control, etc. In the 
future, you might wish to increase the maximum number of iterations if the model does not 
converge. For now, we will simply use the default settings. 
The model run is setup as a steady-state simulation. You can see this defined as follows: 
 Settings under MODFLOW-2005, in the settings tree 
 Type: 3650 for steady-state simulation time 
The MODFLOW-2005 settings tree should look like the figure below: 
 
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Visual MODFLOW Flex Exercise: 3D Capture 
 
 
Note: The ‘Steady-State Simulation Time’ is not used if you 
have selected Transient Flow. However, a number must 
still be entered. Although the simulation will always be run 
to the same equilibrium solution in Steady State, the total 
amount of water passing through boundary conditions 
depends on the amount of time simulated. For example, 
Zone Budget analysis of a Steady State solution would be 
affected by the simulation time, whereas regional head 
values would not. 
Now switch to the Initial Heads option in the translation settings, and specify the initial heads to be 
based on the ground elevation. 
 Initial Heads under MODFLOW-2005, in the settings tree 
 Use Ground Elevation from the list menu for Initial head options 
You are now ready to create the input files (packages) for MODFLOW and MODPATH. 
 button located on the workflow toolbar 
A warning will appear which indicates that steady state models should have at least one specified 
hear or head dependent boundary condition (e.g. drains, river or general head boundary) or it will 
not converge to a solution. Let’s proceed anyway and see what happens: 
 OK to dismiss the warning 
Visual MODFLOW Flex will now create the files necessary to run the USGS MODFLOW and MODPATH 
programs. You will see a progress of the Translation, which should take approximately 5-10 seconds. 
Once complete you will see ‘Translation Finished’ at the bottom of the translation log details window. 
 [Next Step] proceed to the next step in the workflow 
 button located on the workflow toolbar 
The numeric engines will start running and display progress in the main window. MODFLOW-2005 
will run first followed by MODPATH. Each engine will havean information window that displays 
simulation results and progress. Clicking on the tab of the respective window will enable you to view 
detailed results of each run. The tab will show a red X if there is an error with the engine, a galloping 
horse if the engine is currently running, a standing horse if the engine is waiting to run, and a green 
check mark if the engine was run successfully. 
Unfortunately, MODFLOW-2005 will fail to converge in this instance, and you should see the 
following MODFLOW-2005 run log: 
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Visual MODFLOW Flex Exercise: 3D Capture 
 
 
 
The run log indicates that some data may have been excluded, and that no mass balance information 
is available. You can easily open the MODFLOW .LST file from the Visual MODFLOW Flex interface. 
The .LST file contains information about each solution iteration, and can be helpful in determining 
why a model failed. 
 Open Engine Files… button, located above the 
 MODFLOW-2005 and MODPATH-2000 tabs 
 ConceptualModel1.LST select this file 
 Open 
A document will open in Notepad or Wordpad. Scroll through this document and you will quickly 
notice that nearly every cell in the model are dry. 
The reason for this is that all the current boundary conditions in the model are no-flux and the model 
is run under steady state conditions. Steady state problems require at least one constant head (first 
type) boundary condition to serve as a reference head. Transient problems also need a reference 
head, but this is usually provided by the initial condition, and therefore one could use all no-flux 
conditions in a transient case (if it were appropriate). 
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Visual MODFLOW Flex Exercise: 3D Capture 
 
 
Although the reason for failure in this case is obvious, be aware that sometimes the standard solvers 
that come with MODFLOW (PCG2, SIP and SOR) do not converge, even after changing the error 
criterion and number of iterations. The reason is often a poorly posed problem. Reposing the 
boundary conditions, grid, etc. may result in convergence. Sometimes, however, even this doesn't 
work and then the only solution would be another solver or flow model. Besides MODFLOW's 
standard solvers, Visual MODFLOW Flex comes with its own extremely quick and robust solver, the 
WHS solver (BiCGSTAB-P Matrix Solver). Occasionally it fails to converge; fortunately, this is rare. 
Let's add some constant head boundary conditions to the upper and lower boundaries of the model 
(i.e. columns 1 and 36) and re-run the problem under steady state conditions. 
 
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Visual MODFLOW Flex Exercise: 3D Capture 
 
 
PART 6: DEFINE CONSTANT HEAD BOUNDARY CONDITIONS 
 Define Boundary Conditions proceed direct to this step by clicking from 
 the workflow navigator 
Ensure that you are viewing Layer 1 (no Row or Column views): 
  Layer from the list of available views 
 Constant Head from the list of boundary conditions in the Toolbox 
 Assign button under the Toolbox 
 Polyline… from the menu that appears 
 Left-click once in the upper-right cell (i.e. Row 1, Column 1) 
 Right-click once in the upper-left cell (i.e. Row 27, Column 1) 
 Finish 
The Define Boundary Condition window will open, as shown below: 
 
 Next >> to accept default name and continue 
 Type: 240 in the Starting Head (ft) column 
 (or F2) assigns this value to the entire column 
 Type: 240 in the Ending Head (ft) column 
 (or F2) assigns this value to the entire column 
 Finish 
A line or red dots will appear at the upper boundary of the model, indicating that the constant head 
boundary condition has been applied successfully. We will repeat this procedure on the lower 
boundary. 
 Constant Head from the list of boundary conditions in the Toolbox 
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Visual MODFLOW Flex Exercise: 3D Capture 
 
 
 Assign button under the Toolbox 
 Polyline… from the menu that appears 
 Left-click once in the lower-right cell (i.e. Row 1, Column 36) 
 Right-click once in the lower-left cell (i.e. Row 27, Column 36) 
 Finish 
 Next >> to accept default name and continue 
 Type: 240 in the Starting Head (ft) column 
 (or F2) assigns this value to the entire column 
 Type: 240 in the Ending Head (ft) column 
 (or F2) assigns this value to the entire column 
 Finish 
In this example, we will define constant head conditions on the left and right boundaries for all the 
layers from top to bottom. To do this, we will use the copy command: 
 Copy button in the Toolbox 
 Layer from the menu that appears (Layer is the only option) 
The Copy to layer window will open. Simply select the two available constant head boundary 
conditions and apply them to the remaining layers. 
  Copy all/selected groups from the Select boundary group(s) to copy frame 
  Select All Layers from the Select target layer(s) frame 
The Copy to layer window should look like the image below: 
 
 OK to copy the boundary conditions 
 
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Visual MODFLOW Flex Exercise: 3D Capture 
 
 
PART 7: DEFINE ZONE BUDGET ZONES 
Let's add Zone Budget zones to each aquifer so that we can determine the volumetric flows through 
this groundwater flow system. 
 Define Zone Budget Zones proceed direct to this step by clicking from 
 the workflow navigator 
Layer 1 will be left as the default Zone #1 (white). We will assign layer 2 – 8 as Zone #2, layer 9 as 
Zone #3 and layer 10 as Zone #4. Ensure that only the layer view is active: 
  Layer from the list of available views 
 Type: 2 in the Layer field (view layer 2) 
 Assign button in the Toolbox 
 Polygon from the menu that appears 
 Left-click the upper-right cell (i.e. Row 1, Column 1) 
 Left-click the upper-left cell (i.e. Row 27, Column 1) 
 Left-click the lower-left cell (i.e. Row 27, Column 36) 
 Right-click the lower-right cell (i.e. Row 1, Column 36) 
 Finish from the menu that appears 
This will open the Create New Zone Budget Zone window. Click the New button to generate a new 
Zone Budget Zone, and ensure that it is applied to layers 2-8. When finished, the Create New Zone 
Budget Zone window will look like the image below: 
 New to create a new Zone Budget Zone 
  Layers 2-8 ensure layers 2-8 are selected 
 OK 
 
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Visual MODFLOW Flex Exercise: 3D Capture 
 
 
Using the buttons available under the Views frame, slowly go from layer 2 to layer 9. Notice that 
layers 2-8 are now shown in blue, which corresponds to Zone 2 for the Zone Budget calculations. We 
will repeat the process to create Zones 3 and 4 for Layers 9 and 10 respectively. 
  Layer from the list of available views 
 Type: 9 in the Layer field (view layer 9) 
 Assign / Polygon button in the Toolbox 
 Select the entire model area (right-click to complete polygon) 
 Finish from the menu that appears 
 New to create a new Zone Budget Zone 
  Layer 9 ensure layer 9 is selected 
 OK 
 Type: 10 in the Layer field (view layer 10) 
 Assign / Polygon button in the Toolbox 
 Select the entire model area (right-click to complete polygon) 
 Finish from the menu that appears 
 New to create a new Zone Budget Zone 
  Layer 10 ensure layer 10 is selected 
 OK 
Switch to Row view (and readjust the view) and your display should look like the image below: 
 
Now is a good time to save the project. 
 File/Save Project from the main menu 
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Visual MODFLOW Flex Exercise: 3D Capture 
 
 
PART 8: RUN MODFLOW-2005, MODPATH AND ZONE BUDGET 
Let’s try to run our model again, this time including both the MODPATH and Zone Budget engines. 
 Single Run proceed immediately to this step by 
 selecting from the workflow navigator 
  MODPATH from the list of available engines 
  ZONEBUDGETfrom the list of available engines 
 [Next Step] proceed to the next step in the workflow 
 Settings under MODFLOW-2005, in the settings tree 
 Type: 3650 for steady-state simulation time 
 Initial Heads under MODFLOW-2005, in the settings tree 
 Use Ground Elevation for the Initial head options 
 button located on the workflow toolbar 
 [Next Step] proceed to the next step in the workflow 
 button located on the workflow toolbar 
Once again, the numeric engines will start running and display progress in the main window. 
MODFLOW-2005 will run first followed by ZONEBUDGET-2000, and then MODPATH-2000. It should 
only take a few seconds for the engines to run, and you should see a green check mark on the tab 
for each engine, which indicates that it was run successfully. 
This time, the run log for each engine should end with: 
***** The run was successful. ***** 
We will now proceed to the next step of the workflow, and review the results of the model. 
 
 
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Visual MODFLOW Flex Exercise: 3D Capture 
 
 
PART 9: REVIEW MODEL OUTPUTS 
 [Next Step] proceed to the next step in the workflow 
 View Maps 
By default, the equipotential head contour map for layer 1 is displayed. If it is not, ensure that you 
are viewing layer 1, and that the Heads output data object is active: 
  Layer from the list of available views 
 Type: 1 in the Layer field (view layer 1) 
  Heads from the Model Explorer, under Outputs 
With two constant head boundary conditions identical in magnitude and a recharge of 15 
inches/year, a groundwater divide develops in the middle of the first layer. Your display should look 
like the image below: 
 
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Visual MODFLOW Flex Exercise: 3D Capture 
 
 
Please note that the labels on the groundwater contours may be more visible if we turn off the 
gridlines displayed in the 2D viewer. You can turn gridlines on or off by clicking the button above the 
2D viewer. You can also choose whether to display the head results as a smoothed surface (contours 
will be visible) or you can display values on a cell-by-cell basis (no contours will be shown). Use the 
Surface and Cells buttons above the 2D viewer to determine how your results will be displayed. 
Finally, you can use the Cell Inspector to review the exact results in any particular cell. Simply select 
the Cell Inspector by clicking the button above the 2D viewer, then select a cell to inspect. 
 Show/Hide Gridlines button to hide the gridlines 
 Cells button to view head results on a cell-by-cell basis 
 Surface button to return to the surface view 
 (Show Cell Inspector) from the tools above the Viewer 
 Cell values select tab within Cell Inspector 
 Select any cell in model domain 
The cell inspector will display all property attributes, boundary conditions and outputs/results for the 
selected cell. You can customize the information displayed in the cell inspector by adding/removing items 
from the list within the ‘Select Items’ tab within the cell inspector. An example of the cell inspector is shown 
below: 
 
 to close the cell inspector 
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Visual MODFLOW Flex Exercise: 3D Capture 
 
 
Let’s take a moment to review the results of our particle tracking. We’ll review these data in the 3D 
viewer. 
 Note: The particle tracking results may be somewhat 
confusing if reviewed in the Row/Column views. This is 
because our model features a rotation. When viewed in 
Row/Column view you are actually viewing a projection of 
the row/column data onto the true X/Y axes of your model 
domain. In other words, the X/Y model axes do not align 
with the direction of the rows/columns. 
  3D from the list of available views 
 □ Layer to deactivate, from the list of available 
 views 
  Forward Particles from the Model Explorer 
  Backward Particles from the Model Explorer 
 Adjust the view 
 
The 3D viewer should look something like the image below (may vary depending on the orientation 
of your viewer): 
 
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Visual MODFLOW Flex Exercise: 3D Capture 
 
 
PART 10: COMPARING THE CONTAINMENT VOLUME RESULTS WITH THOSE OF 
 THE ORIGINAL PAPER BY LARSON ET AL. (1987) 
The pathline originating at the base of the well screen traces out the approximate maximum extent 
of the containment volume. Compare your results to Figure 1 from Larson et al. (1987) (the horizontal 
scales are different, but can be compared). Your containment volume will be close to theirs but not 
exactly the same. In Larson et al., the containment volume extends about 2400 feet from the well, 
while our results extend a little less than this. The differences can be explained by any of several 
reasons. 
Their boundary conditions may be different from what we used since the original paper 
unfortunately does not provide any information on the boundary conditions used. Another reason 
for the difference could be that we used MODFLOW (presumably more accurate), while they used 
the Trescott and Larson (1976) 3D model. Finally, the pathline model we used was USGS MODPATH, 
while they admittedly used a “simple” pathline scheme. 
Boundary conditions are an important determinant in the shape and location of the containment 
volume. You may be wondering, therefore, what the results would look like if the boundary 
conditions were different. For example, what if there were a no-flux condition on the upper 
boundary (i.e. Column 1) and a constant head of 240 feet on the lower end of the model (i.e. Column 
36). The figure above shows the result you would obtain. They are significantly different from the 
original paper, indicating these were not the boundary conditions used by the authors. See below 
for more on these boundary conditions. 
Larson et al. (1987) defines the containment volume as the volume of groundwater, which 
encompasses all pathlines, terminating at the well. Furthermore, they define a capture zone as a 
horizontal slice of the containment volume at the water table surface or any other depth interval. 
Let's view some capture zones by layer, but remain in the 3D viewer. 
 □ Forward Particles to deactivate, from the Model Explorer 
 Click and drag to reorient the display so that you are looking at a row view, 
from the lower boundary looking ‘up’ (as shown in the image below) 
The backward particles and head surface do interfere with each other, since both are 
red. Let’s make some changes to the active view to make it easier to interpret. We will 
alter the backward pathlines to be more visible (lime green). We will also specify a 
custom interval specifying when a tracking marker should be applied to the pathlines. 
 Right-click Backward Particles from the Model Explorer, under Outputs 
 Settings to open the Settings window 
 Color: Lime Green click the color square to choose a new color 
 + Style expand this option in the settings tree 
 Lines select this option from the settings tree 
 Color: Custom 
 Color: Lime Green 
 OK 
 Right-click Backward Particles from the Model Explorer, under Outputs 
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Visual MODFLOW Flex Exercise: 3D Capture 
 
 
 Pathline Options… to open the Settings window 
A new window (Pathline Option) will open. This window allows you to specify when a tracking 
marker should be drawn. Tracking markers indicate the travel time after a certain time period. Currently, 
the time markers display a marker every 365 days. We will apply a custom interval showing a marker after 
365 days, 730 days, 1825 days and 3650 days. 
  Custom Interval under the Particle Type frame 
 Insert at Cursor button adds new row to table 
 Insert at Cursor hit twice more (total of four rows) 
 Enter times: 365, 730, 1825, 3650 
 OK to accept changes and close window 
Your display should now look similar tothe image below: 
 
Notice how the horizontal area of the capture zone increases with depth due to the high vertical 
anisotropy ratio. Two-dimensional, horizontal models cannot show such a capture zone shape 
changing with depth. 
 
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Visual MODFLOW Flex Exercise: 3D Capture 
 
 
PART 11: REVIEW MASS BALANCE AND ZONE BUDGET RESULTS 
A necessary condition for a successful modeling effort is to have a reasonable mass balance. To look 
at the mass balance results go to the View Charts workflow step: 
 View Charts select this step directly from the workflow navigator 
 OK to dismiss the message about no observation data in 
 the current model run 
 Mass Balance click the button at the top left of the main window 
This will open a general mass balance on your entire model domain. A new window will open which 
itself contains a further four windows, each of which contains a mass balance chart. Let’s reorient 
these charts so that we can review: 
 Window from the main menu 
 Tile 
This will reposition the four charts so that all four can be viewed at once. Your display should look 
like the image below: 
 
The Mass Balance window automatically generates four charts displaying the overall flowrate at the 
specified time (i.e. IN-OUT), the percent discrepancy (i.e. Percent Discrepancy), a time series chart 
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Visual MODFLOW Flex Exercise: 3D Capture 
 
 
of the flow rates (i.e. Time Series; only one data point is available in this case) and the in/out flow 
rate to/from various hydrologic features (i.e. Time step; shows rates for different boundary 
conditions). 
As you can see, there is an excellent mass balance on the model currently, with a residual of 0% (total 
IN and OUT flow = 2.099E8 ft3). You can click any data point to display additional information. You 
can also right-click and select ‘Properties’ to make any desired changed to these charts. 
 to close the Mass Balance window 
Let’s review the mass balance data based on our Zone Budget zones. Assuming the Visual MODFLOW 
Flex interface is still on the View Charts workflow step: 
 Zone Budget click the button at the top left of the main window 
A window very similar to the Mass Balance window will open. The same four charts are displayed, 
although they are now based on the zones previously defined (instead of an overall mass balance on 
the entire model domain). Use the table at the top left to scroll through the zones we defined 
previously and check the mass balance for each zone budget zone. 
It is desirable for the mass balance during a steady state model to be less than 0.1%, but one percent 
is often acceptable. The WHS solver often gives a zero percent discrepancy. Sometimes, however, 
the mass balance discrepancy is ten percent or higher (Anderson and Woessner [1993] cite the 
example of general head boundaries with very high conductances, in which case the mass balance 
error could be over 200%). When the mass balance is too high, the first step to reduce it is to change 
the convergence criteria (typically reducing the criteria by a factor of 10). Also, the maximum 
number of iterations may need to be increased. 
You can change the solver parameters by selecting MODFLOW-2005/Solver in the Run Module. 
Continue reducing the convergence criteria until an acceptable error is achieved. Sometimes, 
because of the nature of a particular problem, certain solvers produce non-converging, oscillating 
results. In these cases, you should try another solver. If the problem still does not converge to an 
acceptable level of error, the model design and/or conceptual model may need to be changed (e.g., 
grid design, material property distributions, repositioning the boundary conditions etc.). Another 
option is to take the final, non-converged results of one solver and use them as a starting condition 
for another solver; this sometimes results in convergence. 
 to close the Zone Budget window 
Now is a good time to save the project. 
 File / Save Project from the main menu 
 
© Waterloo Hydrogeologic Page 48 
Visual MODFLOW Flex Exercise: 3D Capture 
 
 
PART 12: EFFECT OF BOUNDARY CONDITION SELECTION ON THE CONTAINED 
 VOLUME 
In the above example, the left and right boundary conditions were each set equal to 240 feet 
throughout the entire aquifer system thickness. The original Larson et al. (1987) paper provides no 
information on the boundary conditions used. Using two constant-head boundary conditions, as we 
did, seems to give a containment volume close to that presented in their original paper. From a 
practical viewpoint, however, real aquifer systems must have gradients or the groundwater will not 
flow. One reasonable set of boundary conditions then might be a no-flux condition on the left and a 
constant head of 240 feet on the right. If you have time, follow the instructions below to simulate a 
no-flux boundary on the upper boundary (i.e. Column 1), with a constant head boundary on the 
lower boundary (i.e. Column 36). 
But we would also like to preserve the results from our first model run, so instead of overwriting out 
current model run we will clone it. 
 Right-click Run2 in the Model Explorer, under 
 NumericGrid1_refined_refined 
 Clone Model Run… 
A new model run (Run3) and the associated file structure will populate in the Model Explorer, as 
shown below: 
 
© Waterloo Hydrogeologic Page 49 
Visual MODFLOW Flex Exercise: 3D Capture 
 
 
However, we are still viewing the workflow for Run2 (notice how we are still in the same tab, 
NumericGrid1_refined_refined-Run2). In order to open the newly cloned model run: 
 Right-click Run3 in the Model Explorer, under 
 NumericGrid1_refined_refined 
 Open Related Workflow(s)… 
Now that we are on the correct workflow, return to the Define Boundary Conditions workflow step: 
 Define Boundary Conditions from the workflow navigator 
You will arrive at the Define Boundary Conditions workflow step. Select Layer view (Layer 1) and 
ensure that you can see both existing constant head boundary conditions. If necessary, turn 
  Layer: 1 from the list of available views, select layer 1 
 □ Recharge from the Model Explorer, under Boundary Conditions 
 Constant Head select this option under the Toolbox, from the list of 
 available boundary conditions 
 Erase from the Toolbox 
 Group from the menu that appears 
 Select any of the red cells on the upper boundary (these represent ‘Constant Head 1’) 
 Yes to confirm and delete 
You will notice that the boundary conditions in layer 1 have disappeared. You can step through each 
layer to review and ensure that no boundary conditions are present on the upper boundary (Column 
1). Without any boundary conditions specified, by default a no-flux boundary will be applied to the 
upper boundary. 
You can now proceed to translate and run the model: 
 Single Run from the workflow navigator 
  MODPATH from the list of available engines 
  ZONEBUDGET from the list of available engines 
 [Next Step] proceed to the next step in the workflow 
 Settings under MODFLOW-2005, in the settings tree 
 Type: 3650 for steady-state simulation time 
 Initial Heads under MODFLOW-2005, in the settings tree 
 Use Ground Elevation for the Initial head options 
 button located on the workflow toolbar 
 [Next Step] proceed to the next step in the workflow 
 button located on the workflow toolbar 
 [Next Step] proceed to the next step in the workflow 
© Waterloo Hydrogeologic Page 50 
Visual MODFLOW Flex Exercise: 3D Capture 
 
 
 View Maps 
If you view the Heads results at Layer 1, with Backward Particles (change colour to purple) activated, 
then your display will resemble the image below: 
 
Observe the differences between the previous simulation and the altered boundary conditions. The 
figure aboveillustrates these differences, as the groundwater divide no longer exists and the 
containment volume is much larger. 
Now is a good time to save the project. 
 File / Save Project from the main menu 
 
 
***** This concludes the 3D Capture exercise. ***** 
© Waterloo Hydrogeologic Page 51 
Visual MODFLOW Flex Exercise: 3D Capture 
 
 
 
References 
Larson, S.P., C.B. Andrews, M.D. Howland and D.T. Feinstein (1987). Three-Dimensional Modeling 
Analysis of Ground Water Pumping Schemes for Containment of Shallow Ground Water 
Contamination. Proceedings of the Conference on Solving Ground Water Problems with Models, 
Volumes 1 & 2, Denver, CO. National Ground Water Association, Dublin, OH. pp. 517-530 
US EPA, 2002. Elements for Effective Management of Operating Pump and Treat Systems. EPA 
report 542-R-02-009, OSWER 9355.4-27FS. Can be downloaded at http://clu-
in.org/techpubs.htm 
US Army Corps of Eng., 2000. Operation and Maintenance of Extraction and Injection Wells at 
HTRW Sites. Engineers Pamphlet EP 1110-1-27. Can be downloaded at: 
http://www.usace.army.mil 
US EPA, 2008. A Systematic Approach for Evaluation of Capture Zones at Pump and Treat Systems. 
EPA Report 600/R-08/003, Office of Research and Development, National Risk Management 
Research Laboratory, Ada, OK. 
 
http://www.usace.army.mil/
© Waterloo Hydrogeologic 
Visual MODFLOW Flex Exercise: Drumco Part 1 
Conceptual and Numerical Model Development 
 
Exercise Objectives 
1. Create a groundwater flow model by using Visual MODFLOW Flex to generate a 
conceptual model. 
2. Use Visual MODFLOW Flex to import field data and generate surfaces. 
3. Develop a conceptual model domain by generating horizons and structural zones. 
4. Use structural zones to assign flow properties. 
5. Develop the hydrological boundary conditions including rivers, recharge zones, and 
constant heads. 
6. Generate a finite difference grid for a MODFLOW run. 
7. Translate the conceptual model to a MODFLOW numerical model. 
8. Translate and run the MODFLOW model. 
9. Analyze and interpret the results. 
Reference 
US Army Corp of Engineers, 1997. Design guidance for Application of Permeable Barriers to 
Remediate Dissolved Chlorinated Solvents. Publication Number: DG 1110-345-117. Available 
from: https://clu-in.org/download/techfocus/prb/Design-gavaskar-1997.pdf 
Problem Description 
The fictional site you will be simulating is the Drumco buried drum disposal area. The site is 
underlain by an unconfined aquifer, a middle discontinuous confining unit, and a lower semi-
confined aquifer. Both the upper and lower aquifers are used as a source of drinking water by 
homes and industry in the area. 
Buried drums containing industrial degreasing compounds, principally tetrachloroethylene (PCE), 
were discovered during a routine site investigation in 1994. Additionally, gasoline has been 
known to leak from the underground storage tanks. Since then, considerable resources have 
been spent removing the deteriorating drums, characterising the geology and hydrogeology of 
the site, and determining the extent of contamination. A concern is the risk of contamination to 
the lower aquifer, especially with possible degradation products such as vinyl chloride. 
In the 1st part of this exercise we will develop a conceptual site model and perform a preliminary 
groundwater flow analysis. In the 2nd part of the Drumco exercise various remedial schemes will 
be evaluated. 
Conceptual Model Development 
A conceptual model is a simplification of the actual geologic and hydrogeologic conditions that 
captures the essential aspects of the hydrogeologic system. Developing the conceptual model 
is the first step in building a defensible groundwater model because it identifies the features 
Visual MODFLOW Flex Exercise: Drumco – Part 1 
 
© Waterloo Hydrogeologic Page 2 
that control the hydrogeology of the site. The following tasks represent the major steps 
required in the building of a conceptual model: 
• the geography of the site (digital elevation model, site features) 
• subsurface stratigraphy 
• the boundary of the model domain 
• property distribution by hydrostratigraphic unit 
• model domain boundaries 
• model calibration points (head observation wells, concentration observation wells) 
Regional Geography 
The site is situated in a fluvial valley beside a river which acts as a local groundwater discharge 
zone. The digital elevation model for the site is already defined in a grid file (ground.GRD) that 
was developed from the regional digital elevation model (DEM) for the area. 
Hydrostratigraphy 
There were 19 boreholes found in a survey of wells in the area. Analysis of the borehole data 
indicates that subsurface stratigraphy at the site consists of: 
• an upper sand aquifer 
• an intermediate, semi-confining silty-clay aquitard 
• an extensive lower sand/gravel aquifer 
• a lower shale aquitard (that acts as the bottom of the surficial flow system) 
The elevation of the interface for each soil unit, in each of the monitoring wells, was entered 
into an Excel spreadsheet. First, we will open Visual MODFLOW Flex to begin developing our 
conceptual model. 
 
SYMBOLS AND CONVENTIONS 
Symbol Meaning 
 Click the left mouse button 
 Double-click the left mouse button 
 Press the <Enter> key 
 Press the <Tab> key 
In some instances, you will need to click the RIGHT mouse button instead of the left mouse 
button. In this case, the directions will clearly state to click the RIGHT mouse button. 
 
Visual MODFLOW Flex Exercise: Drumco – Part 1 
 
© Waterloo Hydrogeologic Page 3 
Starting Visual MODFLOW Flex 
On your Windows desktop, you will see an icon for Visual MODFLOW Flex. 
Double click Visual MODFLOW Flex to start the program. 
The following Visual MODFLOW Flex window will appear: 
 
 
 
Visual MODFLOW Flex Exercise: Drumco – Part 1 
 
© Waterloo Hydrogeologic Page 4 
SECTION 1: CREATING A NEW PROJECT 
To create a new project, 
 File from the top menu bar 
 New Project… from the top menu bar 
A Create Project dialog box will be displayed prompting you to enter the project name of the 
new Visual MODFLOW Flex project. 
 
 Name Drumco 
 Browse button under Data Repository 
 Select a directory on the hard drive (or use the default location) 
Note: By default, new Visual MODFLOW Flex projects 
will be saved to the following location - 
[C:\Users\<username>\Documents\Visual MODFLOW 
Flex\Projects] 
Under the Units frame (on the right side of the window), make the following changes: 
 cm/s for the conductivity units 
 ft for the length units 
 GPM for the pumping rate units 
 in/yr for the recharge units 
Visual MODFLOW Flex Exercise: Drumco – Part 1 
 
© Waterloo Hydrogeologic Page 5 
 1/ft for the specific storage units 
Once finished, the dialog should appear as shown below: 
 
 
 OK button in the lower right corner of this window. 
The following window will then appear: 
Visual MODFLOW Flex Exercise: Drumco – Part 1 
 
© Waterloo Hydrogeologic Page 6 
 
 Conceptual Modeling button on the left side of the window. 
The new project will then be created and the conceptual modeling workflow will load as shown 
below. 
Visual MODFLOW Flex Exercise: Drumco – Part 1 
 
© Waterloo Hydrogeologic Page 7 
 
Change the start date: 
 5/1/2012 as the model Start Date 
In the middle of the display, you will see a workflow panel that lists the steps required for a 
conceptual model: 
 
Visual MODFLOW Flex Exercise: Drumco – Part 1 
 
© Waterloo Hydrogeologic Page 8 
Above the workflow steps, you will find the main buttons for navigating the workflow: 
 
Next Step (proceed to the next step in the workflow) 
 
Previous Step (return to the previous step in the workflow) 
The first step is to Define the Modeling Objectives; for this exercise, the default objectives are 
fine. 
 Next Stepbutton and the following window will appear. 
 
At this step, you collect the data objects you need for constructing the conceptual model. There 
are several options available: 
• Import Data: import GIS data (shapefiles, CAD files), gridded data, images, points/wells in 
ExcelTM spreadsheets, or XYZ points in text format. 
• Create New Data Object: digitizing new point, polygon, or polyline data objects. 
• Create Surface: interpolate XYZ points using Kriging, Natural Neighbour, or Inverse 
Distance methods. 
For this exercise, you will import all the data objects from external files. 
 
 
Visual MODFLOW Flex Exercise: Drumco – Part 1 
 
© Waterloo Hydrogeologic Page 9 
SECTION 2: IMPORTING RAW DATA 
Import Surfaces 
 
 Import Data 
 
A Data Import dialog box will appear: 
 
 Surface from the Data Type drop down list 
 […] from Source File, to browse to the correct file 
Browse to supporting files folder for this project and select the ground.grd file: 
 ground.GRD 
 Open 
 Next >> from the Data Import Window 
 
In this step you may select the coordinate system of the data being imported. In this exercise, 
we are using local coordinates and all data must be imported into the project in the local 
coordinates. 
 Next >> to continue to the next step 
Visual MODFLOW Flex Exercise: Drumco – Part 1 
 
© Waterloo Hydrogeologic Page 10 
 
This step will prompt you to map any attributes, similar to mapping attributes in a points file. 
This grid file does not contain any attributes so we can continue through the import process. 
 Next >> 
 Finish there are no errors with the file 
The ground surface data object will now appear as a new data object in the Data tab as shown 
below: 
 
Next you will import Surface2.GRD which represents the bottom of the upper aquifer: 
Visual MODFLOW Flex Exercise: Drumco – Part 1 
 
© Waterloo Hydrogeologic Page 11 
 Import Data large button in the middle of the display 
 
A Data Import dialog box will appear. 
 Surface from the Data Type drop down list 
 […] from Source File, to browse to the correct file 
Browse to supporting files folder for this project and select the Surface2.GRD file. 
 Surface2.GRD 
 Open select the file 
 Next accept the default settings 
 Next accept the default settings 
 Next accept the default settings 
 Finish to close the Import window 
Now repeat these Importing Steps to import the remaining Surface data objects: 
 C:\VMODFlex\Drumco\Surface3.txt 
 C:\VMODFlex\Drumco\Surface4.grd 
When you are finished, you should see four surface data objects in the Data Explorer. 
 
You can now visualize these data objects in a 3D viewer. 
 Window/New 3D Window from the main menu 
 
 
The 3D Window appears as a new window within the application; the 
Conceptual Model Workflow remains in its own window. The list of 
available windows is shown as tabs at the top of the display. 
You will now add data objects to this 3D Viewer, by turning them “on” 
  ground add a check-mark beside the ground data object 
Visual MODFLOW Flex Exercise: Drumco – Part 1 
 
© Waterloo Hydrogeologic Page 12 
You should then see the surface in the 3D Viewer. 
Repeat this step for the other surface data objects 
  Surface2 add a check-mark 
  Surface3 add a check-mark 
  Surface4 add a check-mark 
All the surfaces are now visible in the 3D Viewer. Since the default view is plan view, you need 
to rotate the 3D Viewer to visualize all the surfaces. 
 Left click near the bottom of the 3D Viewer 
 Hold down the left-mouse button 
 Drag the mouse upwards 
As you do this, you should see the surfaces from a side-view perspective. 
 
By clicking and dragging the mouse in the viewer window you can position the image however 
you like. You may need to select the rotate button from the toolbar on the right side before 
clicking and dragging the mouse. 
Above the 3D Viewer, you will see a set of standard navigation tools for zoom in/out, pan, and 
Visual MODFLOW Flex Exercise: Drumco – Part 1 
 
© Waterloo Hydrogeologic Page 13 
rotate. 
 
After clicking on a view window to make it active, use the zoom wheel on 
the mouse to zoom in (spin the wheel up) and zoom out (spin the wheel 
down) 
The display will show the selected surfaces that were imported. 
In some cases, you may need to modify the vertical exaggeration of the image. The vertical 
exaggeration is the ratio of the scale to the Y-axis to the scale of the X-axis. This can be 
particularly important for discerning subtle topographic features on surfaces. 
Now we will change the vertical exaggeration of this 3D Viewer. This can be changed at the 
bottom of the viewer window. 
 Type: 40 in the Exaggeration box, located at the bottom 
 of the 3D Viewer. 
Once you do this, the surfaces and their elevations should become much clearer. An example is 
shown below: 
 
The next step is to import the remaining data objects you need for the conceptual model. 
Visual MODFLOW Flex Exercise: Drumco – Part 1 
 
© Waterloo Hydrogeologic Page 14 
Reactivate the conceptual model window as instructed below: 
 Conceptual Model from the tabs of active windows 
 Close ‘3D Viewer – 1’ tab by clicking the ‘x’ button in the tab 
Import Basemap 
We will now import a basemap so that we can review the local setting and familiarize ourselves 
with the project site. 
 Import Data large button in the middle of the display 
 
A Data Import dialog box will appear. 
 Dxf from the data type drop down list 
 […] to browse to the correct file 
Browse to supporting files folder for this project and select the model_area.shp file. 
 DRUMCO.dxf 
 Open select the file 
 Next >> accept the default settings 
 Next >> accept the default settings 
 Finish to close the Data Import window. 
Import Polygons 
 Import Data large button in the middle of the display 
 
A Data Import dialog box will appear. 
 Polygon from the data type drop down list 
 […] to browse to the correct file 
Browse to supporting files folder for this project and select the model_area.shp file. 
 model_area.shp 
 Open select the file 
 Next >> accept the default settings 
 Next >> accept the default settings 
 Next >> accept the default settings 
 Finish to close the Data Import window. 
Note that the model_area now appears in the Data tree. Repeat these steps for other Polygons 
required for this project: 
 Import C:\VMODFlex\Drumco\recharge-areas.shp file, and 
 Import C:\VMODFlex\Drumco\aquitard-hole.shp file 
Visual MODFLOW Flex Exercise: Drumco – Part 1 
 
© Waterloo Hydrogeologic Page 15 
Import Polylines 
Next you will import the polylines that are required for this project: 
 Import Data large button in the middle of the display 
A Data Import dialog box will appear. 
 Polyline from the data type drop down list 
 […] to browse to the correct file 
Browse to supporting files folder for this project and select the constant-head.shp file. 
 constant-head.shp 
 Open select the file 
 Next >> accept the default settings 
 Next >> accept the default settings 
 Next >> accept the default settings 
 Finish to close the Import window 
Repeat these steps for remaining Polylines required for this project: 
 Import C:\VMODFlex\Drumco\River1.shp file, and 
 Import C:\VMODFlex\Drumco\River2.shp file 
These data objects can be displayed in a 2D or 3D Viewer. To load in a 2D viewer: 
 Window/New 2D Window from the main menu 
You will now add data objects to this 2D Viewer, by turning them “on” in the Data explorer 
  model-area add a check-mark 
You should then see the model area polygon in a 2D Viewer. 
Repeat this step for the other polygons, polylines and the site map you just imported 
  recharge-areas add a check-mark in the Data Tree 
  constant-head add a check-mark in the Data Tree 
  River1 add a check-mark in theData Tree 
  River2 add a check-mark in the Data Tree 
  DRUMCO add a check-mark in the Data Tree 
Let’s also change the background color so the objects are easier to review: 
 Right-click background of image 
 Background color from the menu that appears 
 Grey select grey as the background color 
Visual MODFLOW Flex Exercise: Drumco – Part 1 
 
© Waterloo Hydrogeologic Page 16 
Your display should now appear as shown below: 
 
You can adjust the colors of the polylines and polygons through the Settings; 
 model-area right click on the data object in the Data tree 
 Settings… from the pop up menu 
The Settings dialog will appear as shown below 
Visual MODFLOW Flex Exercise: Drumco – Part 1 
 
© Waterloo Hydrogeologic Page 17 
 
Change the color to something new by expanding the Style option in the settings tree and 
selecting the Lines object. Additional style settings are available in the Style node of the Settings 
tree, but are not covered in this exercise. 
 OK to close Settings window. 
You now have all the necessary data to build the conceptual model structure, properties, and 
flow boundaries. This is covered in the next section. 
Before proceeding, please save the project. 
 File/Save Project from the main menu bar 
We must now reactivate the conceptual model window as instructed below: 
 Conceptual Model from the tabs of active windows 
 Close ‘2D Viewer – 1’ tab by clicking the ‘x’ button in the tab 
 (Next Step) from the workflow navigator panel 
This will bring you to the Define Conceptual Model step of the workflow. 
 
Visual MODFLOW Flex Exercise: Drumco – Part 1 
 
© Waterloo Hydrogeologic Page 18 
SECTION 3: BUILDING THE CONCEPTUAL MODEL 
When you arrive at the Define Conceptual Model workflow step you will see the following 
window: 
 
Define Model Area 
The first step in defining the conceptual model is to define the area. 
 Type: Drumco for the Name of the conceptual model 
Now we need to select a polygon data object from the Data tab that represents the boundary 
of the model. We will use the polygon that was imported in the previous section. 
 model-area select this data object from the Data tree 
 under Model Area, from the Define Conceptual 
 Model window 
By selecting the arrow, this will select the model-area polygon as the conceptual model area. 
At this point the Define Conceptual Model window should look like this: 
Visual MODFLOW Flex Exercise: Drumco – Part 1 
 
© Waterloo Hydrogeologic Page 19 
 
 Save top of the Define Conceptual Model window 
Once the conceptual model is created, a new conceptual model tree (named ‘Drumco’) will 
appear in the Model Explorer tab. The conceptual model tree sets up the workflow for structural 
and property modeling, assigning boundary conditions, numerical grid creation and resulting 
numerical models. Expand the conceptual model tree. The conceptual model tree in this exercise 
should appear as follows: 
 
 (Next Step) from the workflow navigator panel 
Save your project. 
 from the main toolbar 
In the next section, you will define the vertical layering for the conceptual model structure. 
Define Model Structure 
Once the conceptual model has been created we proceed to the Define Model Structure 
workflow step. When you arrive at this step the interface will look like this: 
Visual MODFLOW Flex Exercise: Drumco – Part 1 
 
© Waterloo Hydrogeologic Page 20 
 
At this step, you define the vertical geological structure for the conceptual model by converting 
surfaces to horizons. 
Horizons are stratigraphic surfaces that define the upper and lower boundaries of the structural 
zones in a conceptual model. In Visual MODFLOW Flex, horizons are created by clipping or 
extending interpolated surface data objects to the boundary of the conceptual model. 
When horizons are created, structural zones between the horizons will be generated 
automatically. These structural zones can be used later to define the property zones. 
Each horizon surface can be assigned a particular type, which defines the relationship to other 
horizons in the conceptual model. Each horizon type is described below: 
• Erosional horizons can be used as the highest or as an intermediate horizon, but not as 
the bottom of the conceptual model. This type of horizon will truncate all horizons below 
it, including the base horizon. 
• Base horizons can be used as the lowest horizon in the conceptual model. Any 
conformable horizon types will lap onto it, following the elevation of the other horizon, 
while all erosional or discontinuity horizons will truncate it. 
• Discontinuity horizons represent an erosional surface in the middle of a stack of horizons. 
It can never be the highest or lowest horizon. Horizons above it up to the next 
Visual MODFLOW Flex Exercise: Drumco – Part 1 
 
© Waterloo Hydrogeologic Page 21 
discontinuity or erosional horizon will lap onto it, while all horizons below it will be 
truncated by it. These horizons can be thought of as the top or base of a sequence. 
• Conformable (default) horizons will be truncated by erosional, base and discontinuous 
horizons. Lower conformable horizons will be truncated by upper conformable horizons. 
If a conformable horizon is above an erosional horizon, the conformable horizon will 
“conform” to the erosional horizon (it will be pushed up by the erosional horizon). 
 
The horizon rules described above are applied after all the horizons are calculated. If one of the 
horizons will be truncated by an erosional, base, or discontinuity horizon, it is a good idea to 
extend the input data beyond these unconformable horizons in order to truncate them properly. 
Now we will generate horizons from some of the surfaces that we imported in Section 2. 
In the Define Model Structure window, you will provide surface data objects as inputs for 
generating Horizons. 
 (Add) button located above Horizon Information area 
A new row will appear in the Horizon Settings dialog box. 
We must choose a surface to use as the uppermost horizon in the conceptual model. You will 
choose the ground surface from the Data tab. 
 ground select this data object from the Data tab 
 button located in the first column of the Horizon 
 Information area; this will add the ground 
 surface to the Horizons grid 
 
We will add the remaining surfaces to use as horizons in the conceptual model. 
Visual MODFLOW Flex Exercise: Drumco – Part 1 
 
© Waterloo Hydrogeologic Page 22 
 (Add) to add a new horizon 
 Surface2 select this data object from the Data tab 
 
 (Add) to add a new horizon 
 Surface3 select this data object from the Data tab 
 
 (Add) to add a new horizon 
 Surface4 select this data object from the Data tab 
 
 
Now we will change the Type of horizon for uppermost horizon (ground) to Erosional and the 
bottommost horizon (Surface4) to Base. 
In the Horizon Information grid, the Horizon types are defined in the third column: 
 Erosional from the drop-down list, for Horizon1 
 Base from the drop-down list, for Horizon4 
 
You can now preview what the horizons will look like: 
 Preview located above the Horizon Information grid 
The Define Conceptual Model Structure dialog should appear as follows: 
Visual MODFLOW Flex Exercise: Drumco – Part 1 
 
© Waterloo Hydrogeologic Page 23 
 
The horizon preview will display the generated horizons in an adjacent 3D Viewer. The image 
can be rotated by clicking and dragging the mouse within the preview window. 
 Create located above the Horizon Information grid 
This will create the horizons and add these data objects to the Conceptual Model tree. Let’s take 
a moment and view the horizons and structure zones. 
We can view the horizons in a 3D Viewer window. 
 Window/New 3D Window from the main menu 
We can select thehorizons from the Model Explorer and add these to view in the 3D viewer 
window. 
  Horizon 1 select this horizon from the Model Explorer 
  Horizon 2 select this horizon from the Model Explorer 
  Horizon 3 select this horizon from the Model Explorer 
  Horizon 4 select this horizon from the Model Explorer 
We can modify the vertical exaggeration of the viewer window. This option is found at the 
Visual MODFLOW Flex Exercise: Drumco – Part 1 
 
© Waterloo Hydrogeologic Page 24 
bottom of the 3D Viewer window. 
 Type: 40 change the exaggeration of the viewer 
We can rotate the horizons in the 3D Viewer window to see the structure of the conceptual 
model. To rotate the image, click and drag the mouse within the viewer to rotate in the direction 
you wish. Your display should now appear as shown below: 
 
As a result of the horizon creation process, 3D Structure Zones are also created; these volumes 
will form the basis for assigning the flow properties in your conceptual model. 
The structural zones appear in the Model Explorer below the Horizons folder. These zones can 
also be displayed in a 3D Viewer. 
  Zone1 select this Zone from the conceptual model tree 
  Zone2 select this Zone from the conceptual model tree 
  Zone3 select this Zone from the conceptual model tree 
 
Clicking on the  Zones node in the conceptual model tree (the parent 
node) will automatically add/remove the check box for all structural 
Visual MODFLOW Flex Exercise: Drumco – Part 1 
 
© Waterloo Hydrogeologic Page 25 
zones for viewing in the 3D Window. The same approach applies for 
horizons. 
Now remove all the horizons by de-selecting these individually or all at once as explained in the 
tip above. When you are finished, the display will be similar to the one below: 
 
The Zones have settings that include Style settings (color and transparency) and Statistics such 
as volume, area, and spatial extents. More details regarding these options are available in the 
online help. 
Save your project. 
 from the main toolbar 
In the next section, you will define the flow properties for the conceptual model. First, you need 
to re-activate the Drumco workflow window: 
 Drumco from the tabs of active windows 
 Close ‘3D Viewer – 1’ tab by clicking the ‘x’ button in the tab 
Visual MODFLOW Flex Exercise: Drumco – Part 1 
 
© Waterloo Hydrogeologic Page 26 
Define Property Zones 
 (Next Step) from the workflow navigator panel 
This will bring you to the next step in the workflow, Define Property Zones. The following window 
will appear: 
 
By default, Visual MODFLOW Flex automatically assigns the entire model domain with the default 
property parameter values as specified in the Project Settings. In most situations, the flow 
properties will not be uniform throughout the entire model domain and it will be necessary to 
assign different properties to different areas of the model. 
Visual MODFLOW Flex supports various methods for assigning values to property parameters. 
The method used for defining attributes can be defined on the parameter level, allowing you to 
use different methods for different parameters. The supported methods include: 
• Constant value (e.g. Kx = 10 ft/d for the entire formation) 
• Surface data object (2D distribution from a Surfer .GRD, ESRI .GRD, or a surface created 
in Visual MODFLOW Flex by interpolating XYZ points 
• Shapefile attributes 
Visual MODFLOW Flex Exercise: Drumco – Part 1 
 
© Waterloo Hydrogeologic Page 27 
• 3D gridded data object 
In this exercise we will create a new property zone for the formations using constant values. 
 Use Structural Zone within the Create New Property Zone Method 
 area 
 Zone1 highlight this structural zone from the Model 
 Explorer 
 located in the Structural Zones table 
Now define the parameter values in the Property Values grid located in the middle of the display: 
 Type: 0.01 in the Value column for Kx 
 Type: 0.01 in the Value column for Ky 
 Type: 0.001 in the Value column for Kz 
The Define Property Zone window should look like the this: 
 
 Save located on the right side of the display, below 
 the Property Zones table 
Now we will define the property values for the confining layer, Zone 2: 
 Use Structural Zone within the Create New Property Zone Method 
 area 
 Zone2 highlight this structural zone from the 
 Conceptual Model tree 
 located in the Structural Zones table 
Now define the parameter values in the Property Values grid located in the middle of the display: 
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 Type: 5E-6 in the Value column for Kx 
 Type: 5E-6 in the Value column for Ky 
 Type: 5E-7 in the Value column for Kz 
 Save located on the right side of the display, below 
 the Property Zones table 
Now we will define the property values for lower aquifer, Zone 3: 
 Use Structural Zone within the Create New Property Zone Method 
 area 
 Zone3 highlight this structural zone from the 
 Conceptual Model tree 
 located in the Structural Zones table 
Now define the parameter values in the Property Values grid located in the middle of the display: 
 Type: 0.002 in the Value column for Kx 
 Type: 0.002 in the Value column for Ky 
 Type: 0.0002 in the Value column for Kz 
 Save located on the right side of the display, below 
 the Property Zones table 
When you are finished, your display will appear as shown below: 
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Note: that as you create the property zones, these new data 
objects are added to the Conceptual Model tree in the 
Model Explorer 
You can now visualize the property zones in a 3D Viewer. Reopen a 3D Viewer: 
 Window / New 3D Window 
Add the property zones from the conceptual model tree to the viewer: 
  Property Zone 1 select this Zone from the Model Explorer 
  Property Zone 2 select this Zone from the Model Explorer 
  Property Zone 3 select this Zone from the Model Explorer 
 Exaggeration: 40 to improve the view on the y-axis 
 Reorient view by clicking and dragging 
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Save your project. 
 from the main toolbar 
In the next section, you will define the flow boundaries for the conceptual model. First, you need 
to re-activate the Conceptual Model workflow window: 
 Drumco from the tabs of active windows 
 Close ‘3D Viewer – 1’ tab by clicking the ‘x’ button in the tab 
Define Boundary Conditions 
 
 (Next Step) from the workflow navigator panel 
The following window will appear 
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At this stage in the workflow, you have the option to define boundary conditions for the 
conceptual model or proceed on to numerical modeling (Select Grid Type). 
 Define Boundary Conditions 
The following display will appear: 
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At this stage in the workflow, you decide what Boundary Conditions you want to define: 
• Standard: Constant Head, General Head, River, Recharge, etc. 
• Wells 
• Wall Boundaries 
In this exercise we will assign the following boundary conditions: 
1. River boundary along the south and east edge of the model domain 
2. Recharge zones applied to the top of the model domain 
3. Constant Head in the bottom of the domain 
4. Pumping wells 
Define Rivers 
 Define Boundary Conditions 
The following display will appear: 
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Visual MODFLOW Flex provides various methods for assigning the parameter values to boundary 
conditions. Each parameter in the boundary condition can be set to constant or transient and 
values canbe assigned using attributes from various data objects. The available methods for 
assigning boundary condition attributes include using a constant value, using a surface data 
object, using a polygon or polyline shapefile, using a time schedule or using a 3D gridded data 
object. 
Let’s begin by adding a river boundary using the polyline data objects that we imported earlier. 
 River (Type 3 – MODFLOW Only) in the Boundary Condition Type drop 
 down 
We will leave the default boundary condition name (River 1) and the default location (Top). 
The boundary condition location is where the boundary condition will connect on the 
simulation model domain. By selecting Top, this will apply the boundary condition to the top 
layer of the simulation domain. 
Next, we need to define the geometry of the boundary condition by selecting a polyline or 
polygon data object from the Data tab. 
 River1 select this data object from the Data tab 
 button located in the Geometry frame 
You will get an information message indicating that the polyline extends outside the model 
domain. Visual MODFLOW Flex will automatically clip this polyline so it fits inside the 
conceptual model area. 
 OK in the Warning message dialog that appears 
 Next >> in the Define Boundary Condition window 
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The following step in the Define Boundary Condition process is to select how property 
attributes will be defined, and to provide values for the defined boundary condition attributes. 
The following window will appear at this step: 
 
When a polyline data object is selected for defining the geometry of the boundary condition, 
Visual MODFLOW Flex automatically creates a new zone for each individual line in the polyline 
data object (as these can consist of multiple lines). You can also define the values of the river 
boundary at the vertices of the polyline and using linear interpolation between these vertices. 
In this example, we will assign the river boundary parameters to the entire line segment. 
 Show >> to show the line segment in a 2D viewer window 
We will calculate the river stage using the elevation from a surface. The river stage represents 
the free water surface elevation of the surface water body. Under the Stage column, we can 
change from using a constant value to using a surface. 
 Use Surface from the drop-down list under the Stage 
 column 
The From Surface button towards the bottom middle of the dialog box will become active. 
Select this button to choose a surface from the surface data objects in the Data tab. 
 From Surface from the bottom of the dialog box 
The Provide Surface Data dialog will appear and prompt you to choose a surface. Select the 
ground surface grid file that we had imported previously. 
 ground highlight this surface in the Data tab 
 in the Provide Surface Data dialog box 
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The Provide Surface dialog box should appear as follows: 
 
 OK to use this surface data object 
We will use constant values for the remainder of the river boundary condition parameters. 
 Type: 198 as the riverbed bottom 
 Type: 1 as the riverbed thickness 
 Type: 100 as the river width 
 Type: 0.1 as the riverbed conductivity 
We will continue to use the default leakance value which represents the resistance to flow 
between the surface water body and the groundwater caused by the seepage layer. The Define 
Boundary Condition dialog box should look like this: 
 
 Finish to complete the boundary condition creation 
The new river boundary condition object appears as a new object on the conceptual model tree, 
under Boundary Conditions. 
 
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Now you will create a second river boundary condition object, by following the same steps 
above. Return to the Define Boundary Conditions step in the workflow. 
 (Previous Step) from the workflow navigator panel 
 Define Boundary Conditions large button in the middle of the display 
 Define Boundary Conditions large button in the middle of the display 
 
You can also navigate directly to any 
available step (indicated by a green icon) 
in the workflow by selecting any item in 
the Workflow tree. 
 
For example, clicking on Define Boundary 
Conditions item in the workflow explorer 
will take you directly to the appropriate 
step. 
Once you have arrived at this step, the Define Boundary Conditions dialog should appear as 
shown below: 
 
 River (Type 3 – MODFLOW Only) in the Boundary Condition Type drop 
 down 
Now we need to define the geometry of the boundary condition by selecting a polyline or 
polygon data object from the Data tab. 
 River2 select this data object from the Data tab 
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 button located in the Geometry frame 
You will get an information message indicating that the polyline extends outside the model 
domain. Visual MODFLOW Flex will automatically clip this polyline so it fits inside the 
conceptual model area. 
 OK in the Warning message dialog that appears. 
 Next >> in the Define Boundary Condition window 
We will calculate the river stage using the elevation from a surface. Under the Stage column, 
we can change from using a constant value to using a surface. 
 Use Surface from the drop-down list under the Stage 
 column 
The From Surface button towards the bottom middle of the dialog box will become active. 
Select this button to choose a surface from the surface data objects in the Data tab. 
 From Surface from the bottom of the dialog box 
The Provide Surface Data dialog will appear and prompt you to choose a surface. Select the 
ground surface grid file that we had imported previously. 
 ground highlight this surface in the Data tab 
 in the Provide Surface Data dialog box 
The Provide Surface dialog box should appear as follows: 
 
 OK to use this surface data object 
We will use constant values for the remainder of the river boundary condition parameters. 
 Type: 200 as the riverbed bottom 
 Type: 1 as the riverbed thickness 
 Type: 100 as the river width 
 Type: 0.1 as the riverbed conductivity 
 Finish to complete the boundary condition creation 
Now is a good opportunity to save your project. 
 save button from the main toolbar 
Define Recharge Zones 
Now that the river boundary conditions have been created, you will generate the recharge 
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boundary. We will apply this boundary to the entire simulation model domain. 
First you need to return to the Define Boundary Conditions step in the workflow. 
 (Previous Step) from the workflow navigator panel 
 Define Boundary Conditions large button in the middle of the display 
 Define Boundary Conditions large button in the middle of the display 
The Define Boundary Condition dialog box will appear. 
 Recharge (Type 2) in the Boundary Condition Type drop down 
Recharge boundary conditions can only be applied to the top layer of the simulation domain 
and the geometry of the boundary condition must be determined from a polygon. 
Now we need to define the geometry of the boundary condition by selecting a polygon data 
object from the Data tab. 
 recharge-areas select this data object from the Data tab 
 button located in the Geometry frame 
 
Your dialog should appear as shown below: 
 
 Next >> in the Define Boundary Condition window 
When a polygon data object is selected for defining the geometry of the boundary condition, 
Visual MODFLOW Flex automatically creates a new zone for each individual polygon feature 
(shape). 
In this example, we will assign a different recharge attribute to each polygon shape; 
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alternatively, you could map to a shapefile attribute or have recharge data provided by a 
surface (2D distribution, imported from a Surfer .GRD or ESRI .GRD). 
 Show >> to show the recharge polygons in a viewer 
 window 
We will use constant values for the recharge rate. 
 Type: 28 in the table as the Recharge rate for Polygon0 
 
Next you will define the recharge rate for Polygon1. 
 Polygon1 from the list of Polygons in the upper-left corner 
 of the window 
 Type: 18 as the recharge rate for Polygon1 
You will notice that the selected polygon becomes highlighted in yellow in the viewer window 
to help you assign the values correctly. 
 
The Define Boundary Condition dialog box should appear like this: 
 
 Finish to complete the boundary condition creation 
The new Recharge Boundary condition object now appears as a new data object in the conceptual 
model under the Model Explorer, directly below the two River boundary conditions you defined 
previously. 
Define Evapotranspiration 
Now we will define a constant value for Evapotranspiration across the top of the model 
domain. 
First you need to return to the Define Boundary Conditions step in the workflow. 
 (Previous Step) from the workflow navigator panel 
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 Define Boundary Conditions large button in the middle of the display 
 Define Boundary Conditions large button in the middle of the display 
The Define Boundary Condition dialog box will appear. 
 Evapotranspiration (Type 3 – MODFLOW Only) in the Boundary Condition 
 Type drop down 
Select a polyline or polygon data object from the Data tab. 
 model-area select this data object from the Data tab 
 button located in the Geometry frame 
 Next >> in the Define Boundary Condition window 
We will use constant values for the Evapotranspiration rate. 
 Type: 15 in the table as the Evapotranspiration rate 
 Type: 8 in the table for the Extinction Depth rate 
 Finish to complete the boundary condition creation 
The new boundary condition object now appears as a new data object in the conceptual model 
under the Model Explorer, directly below the Recharge boundary condition you defined 
previously. 
Define Constant Head 
Now you will define a Constant Head boundary condition for the bottom of the model domain. 
The general steps are the same as what you followed previously for Rivers 
 (Previous Step) from the workflow navigator panel 
 Define Boundary Conditions large button in the middle of the display 
 Define Boundary Conditions large button in the middle of the display 
The Define Boundary Condition dialog box will appear. You can leave the default boundary 
condition type as Constant Head (Type 1). 
 Bottom from drop-down menu under Where to 
 connect on the simulation model domain 
 
The previous boundary conditions did not require setting “Bottom” as 
the location for the boundary condition; please be sure you have 
defined this step before proceeding otherwise the Constant Head will 
not be assigned to appropriate spot in the conceptual model. 
 constant-head select this polyline data object from the Data tab 
 button located in the Geometry frame 
 Next >> in the Define Boundary Condition window 
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We will use constant values for the Start and End Head parameters. 
 Type: 227 as the Starting Head 
 Type: 227 as the Ending Head 
 Finish to complete the boundary condition creation 
Before proceeding, please save your project. 
 from the main toolbar 
You should now see the following boundary condition objects in the Model Explorer, for your 
conceptual model: 
 
Define Pumping Wells 
Lastly you will define a Pumping Well Boundary Condition object. 
To generate a pumping well boundary condition, you must have a wells data object in the Visual 
MODFLOW Flex project. We will begin by importing a wells data object into this project. 
 File / Import Data… from the main menu bar 
Ensure Well is selected as the Data Type. 
 Well from the Data Type drop down list 
 […] to choose the Source File 
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Browse to supporting files folder for this project and select the Pumping_Wells.xls file. 
 Pumping_Wells.xls 
 Open 
 Next >> 
The next window will show a preview of the data to be imported. 
 
 Next >> 
Visual MODFLOW Flex provides you with various options to import well data. In this window, 
you must select to import the well heads, screens, and pumping schedules: 
  Well heads with the following data 
  Screens (ID, locations) 
  Pumping Schedule 
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 Next >> 
 Next >> to accept the default coordinate system 
The following Data Mapping window will then appear: 
 
In this screen, you need to map the fields from the spreadsheet to required fields. If you 
prepare your ExcelTM file with the exact field names that are required by Visual MODFLOW Flex, 
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no mapping is required and will save you time. For this exercise, the source Excel file has the 
field names assigned as defined in Visual MODFLOW Flex. Take a moment to review the 
required fields for the Wells import on each tab: 
• Well heads: Well ID, XY Coordinates, Elevation, and Bottom 
• Screens: Screen Id, Screen top Z, Screen bottom Z 
• Pump Schedule: Pumping start date, Pumping end date, Pumping rate 
 
When working with your own pumping well data for your models, you 
can use this ExcelTM file as a template. By having all the fields 
automatically mapped this reduces the effort required during the import 
process. 
Since each of the target fields were automatically mapped, you do not need to change the 
Map_to fields or the units. The units are determined based on the project settings. 
Switch to the Screens and Pumping Schedule tabs to review the data requirements associated 
with screen and pumping schedule data. 
 Screens select this tab from the top of the Data Import 
 window as shown below 
 
 Pumping Schedule select this tab from the top of the Data Import 
 window as shown below 
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 Next >> 
The Data Import preview will appear, showing that no errors or warnings were encountered in 
the data file (as indicted by green check marks next to each of the data tabs, and an empty ‘Errors 
and warnings’ dialogue box). 
 
 Finish 
The pumping wells will now appear as a new data object in the Data tree. Take a moment and 
visualize this in the 3D Viewer. 
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Next you need to convert the raw pumping wells data into a conceptual model pumping wells 
object. 
In the Conceptual Model workflow window: 
 Define Pumping Wells from the Workflow tree. 
The following display will appear: 
 
In this step, you need to provide the pumping well data that was previously imported as the data 
source for a conceptual well boundary condition: 
 Pumping_Wells select this data object from the Data tab 
 under Select Raw Wells Data Object or Drag 
 & Drop 
The wells will appear in the preview as show below 
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 OK 
The conceptual model pumping wells will be created and added to the Conceptual Model tree in 
the Model Explorer panel. 
This concludes the Conceptual Model portion of the lab exercise. As you can see from the 
conceptual model workflow, you are now ready to select your grid type andproceed to Numerical 
Modeling. This is covered in the next section. 
Before proceeding, please save your project. 
 from the main toolbar 
 
 
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SECTION 4: DEFINING THE NUMERICAL MODEL 
Once you have created your conceptual model you can create one or more finite difference grids, 
unstructured grids or finite element meshes. Visual MODFLOW Flex supports the creation of 
three different finite difference grid types; deformed, uniform and deformed-uniform. In this 
exercise, we will create a deformed finite difference grid and convert this to a MODFLOW 
numerical model. 
Define MODFLOW Grid 
After completing the previous steps, you should be at the “Select Grid Type” step in the 
workflow. If this is not visible, make the ‘Drumco’ conceptual modeling workflow window 
active… 
 Drumco from the tabs of active windows 
Then select this step in the workflow: 
 Select Grid type from the Workflow tree 
Your display should appear as shown below: 
 
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 Define Finite Difference Grid 
The Define Numerical Grid dialog box will appear: 
 
In this dialog you can provide a unique name for the numerical grid, define a rotation and the 
number of rows and columns. By default, Visual MODFLOW Flex discretizes the horizontal grid 
using 20 rows and 20 columns. We will change the settings of this grid to 40 rows by 40 
columns. 
 Type: 80 for the number of Rows 
 Type: 80 for the number of Columns 
 Next >> 
The next step in numerical grid creation will prompt you to define the vertical grid. First, we 
must choose a grid type as deformed, uniform or semi-uniform. We will leave the grid type as 
deformed. In a deformed grid, the tops and bottoms of the model layers conform to the 
horizon elevation. 
With the deformed grid, a minimum cell thickness must be specified. This must be specified as 
MODFLOW does not permit the lateral discontinuity of layers, a layer cannot have a thickness 
of zero at any point. By setting a minimum thickness, the horizons are shifted based on the 
horizon types that were defined during horizon creation. For this exercise, we will increase the 
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minimum cell thickness to 0.5 ft. 
 
We will refine the topmost zone and bottommost zone into two model layers each. 
 Type: 2 for the Layer Refinement for Zone1 
 Type: 2 for the Layer Refinement for Zone2 
 Type: 2 for the Layer Refinement for Zone3 
 Type: 0.5 for the Minimum Cell Thickness field 
 Apply button located below the Layer Refinement 
 table 
 
 Finish to generate the numerical grid 
The numerical grid will be added as a new data object to the Model Explorer tab under the 
Simulation Domain folder. 
 
The View Finite Difference Grid step in the workflow should now appear as shown below: 
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The Flex Viewer in Visual MODFLOW Flex is a powerful visualization tool for viewing the 
numerical grid and attributes, with different perspectives. 
Under Views, select the views you want to see in the Flex viewer. Visual MODFLOW Flex allows 
you to simultaneously show a Layer, Row, Column and 3D view. Place a check () beside the 
desired view and it will appear on screen. Adjust a specific layer, row or column using the 
up/down arrows. Alternatively, click on the button then click on any specific row, column or 
layer in any of the 2D views, and the selected row, column or later will be set automatically. 
Above the grid view, you will see the standard navigation tools allow you to zoom, pan, and, in 
the case of 3D view, rotate. When you have a Row, Column, or 3D viewer active, you will have 
an option to adjust the Exaggeration. 
 
After clicking on a view window to make it active, use the zoom wheel on 
the mouse to zoom in (spin the wheel up) and zoom out (spin the wheel 
down). 
Take a moment to experiment with the various views that are available for the Finite Difference 
grid. 
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Conceptual Model to Numerical Model Conversion 
Now that you have a grid created, you are ready to populate the grid with data from the 
conceptual model. 
 (Next Step) from the workflow navigator panel 
The following window will appear 
 
 Convert to Numerical Model 
The following progress window will appear 
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 Close to dismiss this dialogue window 
During this step, Visual MODFLOW Flex populates each grid cell with the flow properties, the 
boundary condition parameters (where defined), and the fluxes for the wells. This process may 
take up to 1 minute depending on the speed of your computer. 
The conceptual to numerical conversion creates a new workflow window for the numerical 
model. You should see a new window added to the list of available window tabs at the top of the 
display (the title is NumericalGrid – Numerical Model). The numerical model also has its own 
workflow steps. And finally, a new branch for the numerical model will appear under the Model 
Explorer, listing the various properties, boundary conditions and other inputs for this numerical 
model. These inputs represent the cell-based parameters for the numerical model (cell-based 
property zones, cell-based boundary conditions). These cell representations were defined from 
the conceptual objects, during the conceptual to numerical conversion Your screen should look 
like the image below: 
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The next few sections will cover the steps in the numerical modeling workflow. 
You can return to the conceptual modeling workflow at any time by selecting the ‘Drumco’ tab 
from the list of available windows at the top of the screen. 
 (Next Step) from the workflow navigator panel 
In the next section, you will view the numerical property zones that were generated from the 
conceptual model data. 
Define Properties 
At the Define Properties step in the workflow, the following window will appear: 
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The property zones for the numerical model can be displayed in 2D Layer, Row, and Column 
views, and also in a 3D Viewer. 
The Toolbox located in the middle of the display provides access to the property parameter 
groups and the corresponding parameters: 
• Conductivity: Kx, Ky, Kz. 
• Storage: Ss, Sy, Effective Porosity, Total Porosity 
• Initial Heads 
Different model properties are accommodated by grouping grid cells sharing the same property 
values into “property zones”. Each property zone typically contains a unique set of property 
values and is represented by a different grid cell color. In Visual MODFLOW Flex, each property 
zone can be defined with a constant value or represented by a distribution (range) of values. In 
this exercise, all the property zones are defined with constant values. If, at the time of defining 
the property zones in the conceptual model, you had selected a surface (Surfer .GRD or ESRI 
.GRD) as the data source for a parameter value, then this would result in a distributed property 
zone. 
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The cells can be rendered by the property zone ID (zones) or by a parameter value. Based on 
your selection, the color rendering in the views will change. When you select a parameter for 
rendering (e.g. Kx), you will have an option to color each cell with its discrete value (cells) or to 
have a color shading effect (surface) with contour lines. 
Each of the propertyparameter groups is displayed in the Model Explorer, under the 
Run/Input/Properties folder. This provides you access to the style settings for each parameter 
category and allows you to add properties to a discrete 3D window. 
We will now review the list of property zones: 
 Edit… button under the Toolbox 
The following window will appear: 
 
In the Zones table on the left you can see the property zones that were generated for this 
model based on the conceptual property zones we defined earlier. 
 OK to close the Edit Property window 
We will now show the properties for a selected column: 
  Column add a checkbox beside Column under the Views 
panel 
 Type: 30 in the Column field 
  (Enter key) ok the keyboard 
You should now see a 2D cross-sectional view, along column 30, showing the property values. 
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At the bottom of the display, you will see in the status bar the position of your mouse cursor in 
the current view (XY) grid position (Layer, Row, Column), and the Zone ID. 
 
We will now show the properties in a 3D Viewer: 
  3D add a checkbox beside 3D under the Views panel 
Now remove the layer and column views to maximize the space allocated to the 3D View: 
  Column remove a checkbox beside Column under the 
 Views panel 
  Layer remove a checkbox beside Layer under the Views 
panel 
The 3D view should now occupy the entire space of the “Flex” viewer. Take a moment to rotate 
and zoom on the 3D view. The 3D view shows the properties simultaneously rendered along a 
selected Layer, Row, and Column, which can be defined in the respective field under the Views: 
 Type: 3 in the Layer field 
 Type: 10 in the Row field 
 Type: 30 in the Column field 
As you make changes to the layer, row, and column, the 3D view will automatically update 
based on your selections. To better represent the three “slices” in 3D, you should adjust the 
vertical Exaggeration 
 Type: 30 in the Exaggeration box 
 
When you have the layer, row, or column fields selected, you can also 
use ↑ (up arrow) and ↓ (down arrow) keys on the keyboard to quickly 
change your selection. 
 
Use the same tools as described in the previous step to manipulate the 3D views. Your display 
will now appear as shown below (note: your view may be different depending on the rotation 
angle and zoom). 
 
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When viewing the property zones for model layer 3, you can see that a region in the middle is 
colored green; this represents the “hole” in the aquitard, and the green cells belong to the 
conceptual property zone 3 (the lower aquifer). During the conceptual to numerical 
conversion, Visual MODFLOW Flex automatically assigned the correct conductivity values in this 
pinchout region in the conceptual model. 
Alternatively, you can view the properties along a specific row or column to better see this 
effect: 
  Column add a checkbox beside Column under the Views 
 panel 
 Type: 40 in the Column field 
Your view should now appear as shown below: 
Visual MODFLOW Flex Exercise: Drumco – Part 1 
 
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Use your mouse wheel or the zoom buttons (on the Flex Viewer toolbar) to zoom in on the 
middle of the Column View, to see the region where the pinchout in the model occurs. 
Before proceeding, please save your project. 
 from the main toolbar 
In the next section you will view the boundary condition cells and parameter values for the 
numerical model. 
View Boundary Conditions 
 (Next Step) from the workflow navigator panel 
  Layer add a checkmark beside Layer in the Views 
 panel 
  Column remove a checkbox beside Column under the 
 Views panel 
  3D remove a checkbox beside 3D under the Views 
 panel 
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The following display will appear: 
 
Each boundary condition group of cells will appear as its own node in the model tree. You can 
right click on this to adjust the style settings. In addition, you can load any group of boundary 
condition cells into a stand-alone 3D Viewer. 
Similar to properties, the boundary condition cells can be displayed in any combination of a 
Layer, Row, Column and 3D Views inside the Flex Viewer. 
Under the Toolbox, you will see a drop-down list of boundary condition types supported by 
Visual MODFLOW Flex. Below this you will find an option for editing a single cell or a group of 
cells for the selected boundary condition type. You will recall for this model, we defined a 
constant head, two rivers, and recharge boundary conditions. We will now inspect the 
parameter values for these boundary conditions. 
 River from the toolbox drop-down list 
 Edit button located in the Toolbox 
 Any blue dot in the model in the grid domain, select any river cell 
Visual MODFLOW Flex Exercise: Drumco – Part 1 
 
© Waterloo Hydrogeologic Page 61 
The selected river will become highlighted in the viewer window and the following dialog will 
appear: 
 
You will see the attributes for the river match what was defined for the conceptual river 
boundary condition. The stage will be displayed as a range of values, since it is different for 
each cell as we provided a surface data object in order to calculate the river stage. Please note 
that the selected cell will be highlighted in the Edit boundary condition window. 
 Cancel to close the Edit boundary condition window 
We will now review the constant head value assigned near the bottom of the model domain. 
 Constant Head from the Toolbox drop-down list 
The constant head is located in the bottom of the model; in order to see and edit the cells, you 
must change to Layer 5: 
 Type: 5 in the Layer field, under Views 
  (Enter key) on the keyboard 
You should then see a line of red points along the top of the model domain, which represent 
the constant head cells. 
 Edit from the Toolbox 
 Any red dot in the model in the grid domain, select a constant head cell 
The selected constant head boundary condition will become highlighted and the Edit Boundary 
Condition Attributes dialog will appear; take a moment and review the values, then close the 
dialog when you are finished. 
Visual MODFLOW Flex Exercise: Drumco – Part 1 
 
© Waterloo Hydrogeologic Page 62 
 Cancel to close the Edit boundary condition window 
 
We will now review the recharge values that are assigned for the model. Recharge is assigned 
to the top of the model domain (layer 1), return to viewing layer 1: 
 Type: 1 in the Layer field, under Views 
  (Enter key) on the keyboard 
 Recharge from the Toolbox drop-down list 
Ensure Recharge is also selected in the Model Explorer. 
  Recharge 1 
The Recharge zonation should then appear in the Layer view. 
 
 Database button under the Toolbox 
The following window will appear: 
 
Visual MODFLOW Flex Exercise: Drumco – Part 1 
 
© Waterloo Hydrogeologic Page 63 
 
You can see the recharge zones that were generated for this model are based on the 
conceptual recharge polygons we defined earlier. One additional property zone is added, which 
has an undefined value for all the regions where user-defined recharge values were not added 
(the inactive cells). 
 Cancel to close the Database window 
We have now reviewed the numerical model inputs for the MODFLOW model. Before we can 
proceed to running the simulation, we need to define calibration points (head observations) for 
the model. This is covered in the next section. 
Define Observation Wells 
Field observations of groundwater heads and fluxes are essential in order to calibrate the results 
obtained by MODFLOW. In this exercise, you will add several head observations wells, and 
analyze these against the corresponding calculated valuesafter the model run is complete. First, 
we need to import the observation wells: 
 File / Import Data… from the main menu bar 
 Well as the data type 
 […] to choose the Source File 
Browse to supporting files folder for this project and select the Observation_Wells.xls file. 
 Observation_Wells.xls 
 Open 
 Next >> 
A preview window will appear displaying the source data. 
Visual MODFLOW Flex Exercise: Drumco – Part 1 
 
© Waterloo Hydrogeologic Page 64 
 
 Next >> 
Visual MODFLOW Flex provides you with various options to import well data. 
  Well heads with the following data 
  Observation points 
  Observed heads 
Ensure you have the options selected as shown below. 
 
Visual MODFLOW Flex Exercise: Drumco – Part 1 
 
© Waterloo Hydrogeologic Page 65 
 Next >> 
 Next >> to accept the default Coordinate System 
In the Data Mapping screen you need to map the fields from the spreadsheet to the required 
fields in the Wells Import utility. To save time, you can prepare your ExcelTM file with the exact 
file names that are required by Visual MODFLOW Flex, and then no mapping is required. For 
this exercise, the source ExcelTM file has the map names pre-defined. Take a moment to review 
the required fields for the wells import: 
• Well heads: Well Id, X and Y Coordinates, Elevation, and Well bottom 
• Observation Points: Logger ID, Elev., Observation date, Observed head 
Confirm the units for the source file to match the project units, lengths should be assigned as 
feet. 
 Next >> to accept the mappings 
The Data Import preview will appear: 
 
 Finish 
The Observation_Wells will now appear as a new data object in the Data tree. Take a moment 
and visualize this in the 3D Viewer. 
Next you need to add these raw observation wells as observation points to the numerical model. 
 
 (Next Step) from the workflow navigator panel 
Visual MODFLOW Flex Exercise: Drumco – Part 1 
 
© Waterloo Hydrogeologic Page 66 
The following display will appear: 
 
 Define Observation Wells 
Since you have the observation wells already imported, you only need to map these to the 
numerical model. 
 Observation_Wells select this data object from the Data tab 
 under Select Observation Object in the Toolbox 
The observation wells will be added to the display and the numerical model tree. Take a moment 
to scroll through the layers in the model to see observed heads for the various numerical model 
layers. You should see several green points in the model domain that represent the observed 
head at that location. 
The following figure shows the observation points for Layer 2 
Visual MODFLOW Flex Exercise: Drumco – Part 1 
 
© Waterloo Hydrogeologic Page 67 
 
Before proceeding, please save your project. 
 from the main toolbar 
You now have all the inputs defined for the numerical model in order to run the MODFLOW-
2005 simulation. In the next section you will translate the model inputs into MODFLOW 
package files, and then run the MODFLOW engine. 
 
Visual MODFLOW Flex Exercise: Drumco – Part 1 
 
© Waterloo Hydrogeologic Page 68 
SECTION 5: RUNNING MODFLOW-2005 
 (Next Step) from the workflow navigator panel 
 Single Run 
The following display will appear: 
 
 
At this step, you can choose what version of MODFLOW to run and also to optionally include 
Zone Budget and MODPATH. For this exercise, the defaults are settings are used. 
 (Next Step) from the workflow navigator panel 
Translation Settings 
The Translation settings will load as shown below: 
Visual MODFLOW Flex Exercise: Drumco – Part 1 
 
© Waterloo Hydrogeologic Page 69 
 
At the Translate step you have the option to adjust the various parameters and flags for the 
MODFLOW packages and run time settings. Available options include: 
• General Settings 
• Time Steps (only appropriate for transient simulations) 
• Solvers 
• Recharge and EVT 
• Lake 
• Layers 
• Rewetting 
• Initial Heads 
• Anisotropy 
• Output Control 
For this exercise, we need to make the following changes. First, change the solver to GMG: 
 Solvers in the translation settings window, under 
 MODFLOW-2005 
 GMG from the Selected Solver drop-down list 
Next, activate Rewetting: 
Visual MODFLOW Flex Exercise: Drumco – Part 1 
 
© Waterloo Hydrogeologic Page 70 
 Rewetting in the translation settings window, under 
 MODFLOW-2005 
 Active from the Cell wetting drop-down list 
Change the Initial Heads settings 
 Initial Heads in the translation settings window, under 
 MODFLOW-2005 
 Use Ground Elevation from the Initial head options drop-down list 
You are now ready to translate the inputs to the MODFLOW packages. 
 to translate MODFLOW-2005 input files 
The translation will begin, it should complete in approximately 5-10 seconds. At this stage, if any 
errors or warnings are encountered with any of the packages, you will be notified in the message 
log. 
 
When you are working with a more refined model grid and/or a transient 
model with many stress periods, you should expect the translation times 
to be a little longer. 
When the Translation is complete, you should see a full log of the translation process and a final 
message at the bottom of the Translation log which says: 
############# Translation Finished ############# 
 (Next Step) from the workflow navigator panel 
Run Numerical Engines 
You may now start running the MODFLOW-2005 engine: 
 to run the model engines 
The MODFLOW-2005 engine will start running and show progress of the time step and iterations 
in the main window. 
When the MODFLOW-2005 engine is finished, you should see a message “***** The run was 
successful. *****” in the progress window, as shown below. 
Visual MODFLOW Flex Exercise: Drumco – Part 1 
 
© Waterloo Hydrogeologic Page 71 
 
In addition, two new items will appear on the Model Explorer under the Outputs: Head and 
Drawdown. In the next section, you will view the contours and color shading of the calculated 
heads and assess the model calibration by comparing the calculated heads to the observed 
values. 
 
Visual MODFLOW Flex Exercise: Drumco – Part 1 
 
© Waterloo Hydrogeologic Page 72 
SECTION 6: VIEW AND ANALYSE RESULTS 
 (Next Step) from the workflow navigator panel 
 View Maps 
View Maps 
The following display will appear: 
 
The Flex Viewer will show the calculated heads, with contours, in layer 1; the color legend 
under the Toolbox helps you to correlate the color distribution to a head value. 
 
We will now show the Heads along a selected column: 
Visual MODFLOW Flex Exercise: Drumco – Part 1 
 
© Waterloo Hydrogeologic Page 73 
  Column add a checkbox beside Column under the Views 
 panel 
 Type: 40 in the Column field 
  (Enter key) 
Turn off the Layer view: 
  Layer remove checkbox beside Layer under the Views 
 panel 
You should see a cross-section along column 40 showing the calculated heads. Take a moment 
to use the navigational tools to zoom and pan. Please note that you can use the cell inspector 
tool to review the results for any particular cell. 
 (Show Cell Inspector) from the tools above the Viewer 
 Cell values select tab within Cell Inspector 
 Select any cell in model domain 
The cell inspector will display all property attributes, boundary conditions and outputs/results 
for the selected cell. You can customize the information displayed in the cell inspector by 
adding/removing items from the list within the ‘Select Items’ tab within the cell inspector. 
 
Next, restore just the Layer view for the Flex viewer: 
  Layer add a checkbox beside Column under the Views 
 panel 
  Column remove checkbox beside Column under the Views 
 panel 
Now we will visualize the drawdown. 
  Heads remove the checkbox beside Heads in the Model 
 Explorer, under the Outputs folder 
  Drawdown add thecheckbox beside Drawdown in the Model 
 Explorer, under the Outputs folder 
The Drawdown will now appear in the display. Let’s take a moment and adjust the contour 
interval: 
 Right-click on Drawdown in the Model Explorer, under the Outputs folder 
 Settings from the pop-up menu that appears 
The following window will appear: 
 
Visual MODFLOW Flex Exercise: Drumco – Part 1 
 
© Waterloo Hydrogeologic Page 74 
 
 Style from the Settings tree on the left 
 Contour Line item under the Style menu 
Visual MODFLOW Flex Exercise: Drumco – Part 1 
 
© Waterloo Hydrogeologic Page 75 
 
 Type: 1 for the Contour Interval value 
 OK 
The Drawdown contours should now appear as shown below. Use the options in the Flex 
viewer to scroll through the Drawdown for various layers. 
Visual MODFLOW Flex Exercise: Drumco – Part 1 
 
© Waterloo Hydrogeologic Page 76 
 
View Charts 
 View Charts from the workflow tree 
Visual MODFLOW Flex allows you to display time series and calibration (observed heads vs. 
calculated heads) charts. The settings in the middle of the display allow you to choose the chart 
type and select which wells to display on the selected chart. 
 
Visual MODFLOW Flex Exercise: Drumco – Part 1 
 
© Waterloo Hydrogeologic Page 77 
 
 
For this exercise, you will view the calibration for each layer: 
  Layer #5 add a check next to Layer 4 in the Observations 
 panel 
 Apply button located at the bottom of the Chart 
 settings panel 
Visual MODFLOW Flex automatically finds all the observation points that lie within Layer 4, and 
displays this on the chart. The display should now appear as shown below: 
 
Visual MODFLOW Flex Exercise: Drumco – Part 1 
 
© Waterloo Hydrogeologic Page 78 
 
You can see that the fit for Layer 4 is pretty reasonable. 
Next add the wells for Layer 1. There is only one observation point in Layer1, and it shows a 
reasonably good calibration. 
  Layer #1 add a check next to Layer 1 in the Observations 
 panel 
 Apply button located at the bottom of the Chart 
 settings panel 
Finally, add the Observations for Layer 2: 
  Layer #2 add a check next to Layer 2 in the Observations 
 panel 
 Apply button located at the bottom of the Chart 
 settings panel 
The calibration chart should look like the image below: 
Visual MODFLOW Flex Exercise: Drumco – Part 1 
 
© Waterloo Hydrogeologic Page 79 
 
You will see that the calibration is not quite as good for some regions in Layer 2; the model is 
over-calculating the heads when compared to the field measurements. This is something that 
should be investigated as part of the model calibration process, however this outside the scope 
of this exercise. 
Now is a good time to save your project. 
 from the main toolbar 
 
 
***** This concludes the ‘Drumco: Part 1’ exercise. ***** 
 
 
Visual MODFLOW Flex Exercise: Drumco – Part 1 
 
© Waterloo Hydrogeologic Page 80 
SECTION 7: OPTIONAL EXERCISES 
If time permits, you may experiment with some additional options in Visual MODFLOW Flex: 
View Zone Budget Charts 
1. Return to the Single Run step (where you chose the MODFLOW-2005 engine) 
2. Select the Zone Budget engine to be included with the model run 
3. Repeat the Translate and Run Engines step 
4. View Charts 
5. Select the Zone Budget button at the top of the charts window; take a few minutes to 
review the in/out flows between the various sources and sinks 
Generate another MODFLOW Model 
1. Return to the conceptual model workflow (Drumco tab), and select the grid type step 
2. Create a new MODFLOW grid, and experiment with different horizontal or vertical 
resolutions (e.g. 100 rows * 100 columns), or more vertical layering 
3. Re-run the conceptual to numerical conversion 
4. Review the resulting properties and boundary condition cells 
5. Re-translate and run engines 
6. View and analyze the results 
 
© Waterloo Hydrogeologic 
Visual MODFLOW Exercise: Drumco Part 2 
Risk Assessment and Remediation Feasibility Design 
 
Exercise Objectives 
In this exercise you will use a three-dimensional, steady-state groundwater flow model created 
with Visual MODFLOW Flex as a tool for risk assessment and remediation design. You will 
continue using the model created in Part 1 of the Drumco exercise. You will also use the Visual 
MODFLOW Flex 3D Viewer to examine your model results in 3D. The following major objectives 
will be completed during this exercise: 
Risk Assessment 
• Using the particle tracking features in Visual MODFLOW, determine whether the local 
water supply wells are at risk of contamination by the groundwater plume migrating 
from the Drumco disposal area. 
Remediation Design Feasibility 
• Examine the effects of installing a pumping well to capture the groundwater plume and 
determine an optimal well location and pumping rate. 
• Evaluate the benefits of installing horizontal flow barriers to isolate the contaminated 
area. 
• Explore the results of installing an interceptor trench to capture the shallow 
groundwater plume. You will try two system designs with different trench depths to 
capture the groundwater plume while removing as little uncontaminated water as 
possible – thus avoiding the cost of treating uncontaminated water in your treatment 
system. 
• Visualize the effects of installing a funnel-and-gate remediation system. You will 
experiment with a simple funnel-wall design to capture the groundwater plume, and 
obtain an estimate of the flow-rate through the treatment cell. The flow-through rate is 
needed to calculate the life span of the reactive materials used in the treatment 
process. 
Reference 
General Methods for Remedial Operations Performance Evaluations, US EPA, Office of Research 
and Development, EPA/600/R-92/002, January 1992. 
In Situ Remediation of Contaminated Ground Water: The Funnel-and-Gate System, Starr, Robert 
C, and Cherry, John A., 1994. Ground Water, Vol. 32, No. 3. National Ground Water 
Association. 
US Army Corp of Engineers, 1997. Design guidance for Application of Permeable Barriers to 
Remediate Dissolved Chlorinated Solvents. Publication Number: DG 1110-345-117. Available 
from: https://clu-in.org/download/techfocus/prb/Design-gavaskar-1997.pdf 
https://clu-in.org/download/techfocus/prb/Design-gavaskar-1997.pdf
Visual MODFLOW Exercise: Drumco – Part 2 
 
© Waterloo Hydrogeologic Page 2 
Problem Description 
The fictional site you will be simulating is the Drumco buried drum disposal area. The site is 
underlain by an unconfined aquifer, a middle discontinuous confining unit, and a lower semi-
confined aquifer. Both the upper and lower aquifers are used as a source of drinking water by 
homes and industry in the area. 
Buried drums containing industrial degreasing compounds, principally tetrachloroethylene (PCE), 
were discovered during a routine site investigation in 1994. Additionally, gasoline has been 
known to leak from the underground storage tanks. Since then, considerable resources have 
been spent removing the deteriorating drums, characterising the geology and hydrogeology of 
the site, and determining the extent of contamination. A concern is the risk of contamination to 
the lower aquifer, especially with possible degradation products such as vinyl chloride. 
In the 1st part of this exercise a conceptual site model was created, and preliminary groundwater 
flow analysis was performed. In the 2nd part of the Drumco exercise various remedial schemes 
will be evaluated. 
Regional Geography 
The site is situated in a fluvial valley beside a river which acts as a local groundwater discharge 
zone. The digital elevation model for the site is already defined in a grid file (ground.GRD) that 
was developed from the regional digital elevation model (DEM) for the area. 
Hydrostratigraphy 
There were 19 boreholes found in a survey of wells in the area. Analysis of the borehole data 
indicates that subsurfacestratigraphy at the site consists of: 
• an upper sand aquifer 
• an intermediate, semi-confining silty-clay aquitard 
• an extensive lower sand/gravel aquifer 
• a lower shale aquitard (that acts as the bottom of the surficial flow system) 
The elevation of the interface for each soil unit, in each of the monitoring wells, was entered 
into an Excel spreadsheet. First, we will open Visual MODFLOW Flex to begin developing our 
conceptual model. 
SYMBOLS AND CONVENTIONS 
Symbol Meaning 
 Click the left mouse button 
 Double-click the left mouse button 
 Press the <Enter> key 
 Press the <Tab> key 
In some instances, you will need to click the RIGHT mouse button instead of the left mouse 
button. In this case, the directions will clearly state to click the RIGHT mouse button. 
Visual MODFLOW Exercise: Drumco – Part 2 
 
© Waterloo Hydrogeologic Page 3 
Starting Visual MODFLOW Flex 
On your Windows desktop, you will see an icon for Visual MODFLOW Flex. 
Double click Visual MODFLOW Flex to start the program. 
The following Visual MODFLOW Flex window will appear: 
 
 
Visual MODFLOW Exercise: Drumco – Part 2 
 
© Waterloo Hydrogeologic Page 4 
PART 1: OPENING AN EXISTING PROJECT 
Ideally, Part 2 of the Drumco exercise will follow on your results from Part 1. If you have 
completed Part 1 of the Drumco exercise (i.e. the creation of a conceptual model) then 
continue from Part 1. However, if Part 1 wasn’t completed you can use the solution file for Part 
1 provided as part of the supporting files. To open an existing project, 
 File from the top menu bar 
 Open Project… from the top menu bar 
A Select the Project File window will be displayed prompting you to browse to and open the 
existing project. Go to the location of the Drumco exercise from Part 1 of this exercise, or 
alternatively you can open the solution file which was provided in the supporting files folder. 
When you reopen the Drumco project the Visual MODFLOW Flex interface will bring you to the 
workflow step that was open when the project was last opened. You should see the following 
display, which represents the last step in Drumco – Part 1 (you may see a different workflow 
step, it all depends on which step you had worked on most recently): 
 
Before proceeding with our remediation scenarios, take a few moments to explore the different 
Visual MODFLOW Exercise: Drumco – Part 2 
 
© Waterloo Hydrogeologic Page 5 
steps in the numerical modelling workflow and to familiarize yourself with the distribution of 
parameters and boundary conditions within the model domain. 
 Define Properties from the workflow navigator 
 Edit under Toolbox to view conductivity values 
 Cancel to close 
 Define Boundary Conditions from the workflow navigator 
 River from the Toolbox dropdown menu to view the river 
 in Layer 1 
 Constant Head from the Toolbox dropdown menu 
 Type: 6 under Layer in the Views menu to view the 
 Constant Head in Layer 6 
When you are finished we will proceed to the next step, which is to add particles to the model 
and run a MODPATH simulation. 
 
 
 
Visual MODFLOW Exercise: Drumco – Part 2 
 
© Waterloo Hydrogeologic Page 6 
PART 2: PREFERRED FLOW PATHWAYS AND RISK ASSESSMENT USING 
 MODPATH 
In this section a row of particles will be added to the model domain at the source location of 
the contaminant plume. You will run a MODFLOW and MODPATH simulation to gain insight into 
where the contaminant particles will travel at your site. 
Adding Particles 
 Define Particles from the workflow navigator 
When you arrive at the Define Particles workflow step you will see the following window: 
 
We will be assigning the particles manually, and we would like to assign them to the cells 
corresponding with the location of the underground storage tank. To make this easier, we’ll 
overlay the 2D viewer with our sitemap: 
 Right-click background of image 
 Background color from the menu that appears 
 Grey select grey as the background color 
Visual MODFLOW Exercise: Drumco – Part 2 
 
© Waterloo Hydrogeologic Page 7 
  DRUMCO add a check-mark in the Data Tree 
 [Zoom to Box] zoom around the area of the Drum Disposal Area 
 Assign button under Toolbox 
 Point from the list menu that appears 
 Draw a line of particles along the lower edge of the Drum Disposal Area (see image 
below) 
 Finish button under Toolbox 
The Create New Particles window will open, as shown below: 
 
  Forward specify forward particles 
  Layer 2 apply to Layer 1 and Layer 2 
 OK to accept remaining settings and generate particles 
You should see a line of green dots in the cells at the source of the PCE plume, as shown below: 
Visual MODFLOW Exercise: Drumco – Part 2 
 
© Waterloo Hydrogeologic Page 8 
 
 Finish button under Toolbox 
The particles have now been defined successfully, and we’re ready to proceed to the next 
steps; translating MODFLOW files and running the model. 
Running MODFLOW-2005 and MODPATH 
To run a simulation with the existing model data set we will proceed to the single run step in 
the workflow: 
 Single Run from the workflow navigator 
Visual MODFLOW Exercise: Drumco – Part 2 
 
© Waterloo Hydrogeologic Page 9 
You will be transferred to the engine selection screen. The window appears listing the available 
groundwater flow engines (MODFLOW-2005, MODFLOW-2000, MODFLOW-LGR, MODFLOW-
NWT or MODFLOW-SURFACT), water budget engines (ZoneBudget), particle tracking engines 
(MODPATH) and contaminant transport engines (if applicable, not in this case). The engine 
selection screen is shown below: 
 
For this simulation, both MODFLOW 2005 and MODPATH will be run. 
 USGS MODFLOW 2005 from WH from the list of available engines 
  MODPATH ensure MODPATH will also run 
 (Next Step) from the workflow navigator panel 
 to translate input files 
 (Next Step) from the workflow navigator panel 
 to run the model engines 
Visual MODFLOW Exercise: Drumco – Part 2 
 
© Waterloo Hydrogeologic Page 10 
Visual MODFLOW will first translate the input files from Visual MODFLOW’s format to the 
necessary format required by MODFLOW 2005 and MODPATH. Once the translation is 
completed, Visual MODFLOW will run the MODFLOW 2005 and MODPATH programs to 
compute the simulation results. The engine should finish running in just a few seconds. The run 
log will indicate that “***** The run was successful. *****”, as shown below. 
 
Visualizing the Results in 2D 
To visualize the modelling results: 
 (Next Step) from the workflow navigator panel 
 View Maps 
Your display will look like the image below, showing the simulated head values in layer 1 of the 
model. 
Visual MODFLOW Exercise: Drumco – Part 2 
 
© Waterloo Hydrogeologic Page 11 
 
Before going further with an analysis of output, let’s look at the model calibration to 
groundwater heads. We will compare the observed heads (in the Head Observations wells) and 
the calculated heads: 
 View Charts from the workflow navigator 
  Labels to clear all labels from the view 
  All Times from the Observations menu 
  All Obs. from the Observations menu 
 Apply 
And the following calibration graph will appear: 
Visual MODFLOW Exercise: Drumco – Part 2 
 
© Waterloo Hydrogeologic Page 12 
 
The calibration shows a significant source of error, with the calculated heads regularly falling 
below the observed values. A normalized root mean squared error of <10% is desirable. For the 
purposed of this exercise the calibration will suffice. 
To determine if any of the sensitive down-gradient receptors are at risk from the groundwater 
contamination, you will now evaluate the preferred flow pathways of forward tracking 
particles. To display the particle pathlines: 
 View Maps from the workflow navigator 
  Forward Pathlines from the Model Explorer, under Outputs 
Thiswill display, in plan view, all pathlines from every layer as shown on the following page. 
Recall when the model was built, forward tracking particles were placed at the location 
corresponding to the drum disposal area (in Layer 1 and Layer 2) to track advective flow 
Visual MODFLOW Exercise: Drumco – Part 2 
 
© Waterloo Hydrogeologic Page 13 
directions from the Drumco Site and determine the preferential migration pathways of the 
groundwater plume. At first glance, the flow pathlines display will look a little peculiar, as some 
of the forward tracking particles from the drum disposal area appear to have an unnatural bend 
in flow direction. However, closer examination of the flow pathlines will explain why these 
pathlines bend. 
 
There is a zone of discontinuity in the middle layer where the confining unit pinches out. In this 
area, the upper aquifer is directly connected to the lower aquifer. The forward tracking 
pathlines indicates they are all travelling downwards into the lower aquifer, and eventually into 
the industrial water supply well, through this pinchout and the surrounding area where Zone2 
Visual MODFLOW Exercise: Drumco – Part 2 
 
© Waterloo Hydrogeologic Page 14 
becomes very thin. To view this in cross-section, 
  Column under the Views menu 
 Type: 19 for the column number (this is the column with the 
 pumping well) 
  Wells from the Model Explorer to make the well visible 
Zoom in to the area around the particle pathlines. The screen display should look similar to the 
figure below. This cross-sectional view displays the pathline projections as one looks into the 
screen from north to south across the site. 
Note: some changes have been made to the viewer which 
were not listed here (e.g. changing particle pathline color). 
You may perform these changes yourself by right-clicking 
the desired object in the Model Explorer and selecting 
Settings. Most visualization settings are set through this 
menu. 
Visual MODFLOW Exercise: Drumco – Part 2 
 
© Waterloo Hydrogeologic Page 15 
 
To illustrate the different hydraulic conductivities found in the subsurface: 
  Conductivity in the Model Explorer under Properties 
As you can see, the particle pathlines move through three different hydraulic conductivity 
zones (K1, K2, and K3). Each zone has a different impact on the particles as they travel through 
the subsurface. Please note that you may have to deactivate/reactivate particle pathlines 
and/or wells in order to display them again. 
Visual MODFLOW Exercise: Drumco – Part 2 
 
© Waterloo Hydrogeologic Page 16 
 
To return to the plan view of the output, 
  Layer in the Views menu to go to the Layer view 
  Column to deactivate the column view 
To determine how long it would take for the contaminant plume to reach the pumping well 
(assuming advective transport only), you can plot time markers directly on the pathlines. The 
time markers are indicated by the dots on the pathlines. To set the frequency between time 
markers: 
 Right-Click Forward Pathlines from the Model Explorer under Outputs 
Visual MODFLOW Exercise: Drumco – Part 2 
 
© Waterloo Hydrogeologic Page 17 
 Pathline Options… from the menu that appears 
A Pathline Options dialogue box will appear as shown below. As you can see, the particle 
pathlines are already set to display a tracking marker every 1 year (365 days), which is very 
helpful for determining the approximate travel time to reach an interceptor. 
 
 Cancel to close the window 
If you count the time markers, the results indicate that the plume will reach pumping well 
IWSW-12a in less than 4 years (particles from layer 1). To count the time markers, it may be 
easier to zoom in on the area around the pumping well and drum disposal area as displayed in 
the figure on the following page. 
 [Zoom to Box] from the tool bar menu above the display 
Move the mouse pointer into the model domain and click on any location northwest of the area 
to anchor the zoom window. Then stretch a box around the area and click again to close the 
zoom window. Counting the particles may also be easier in 3D. Take some time to review the 
results. 
We can also display the hole in the zone 2 aquitard by activating this polygon data object from 
the Data Tree. It will be easier to view if you also change the colour of this object. Your screen 
should look something like the image below: 
  aquitard-hole activate from the Data Tree (change colour to black) 
Visual MODFLOW Exercise: Drumco – Part 2 
 
© Waterloo Hydrogeologic Page 18 
 
As you can see, only a few of the particles actually go through the aquitard hole. The remainder 
seem to pass through zone 2 just to the left of the aquitard hole. This is because the zone is 
very thin in this area. Let’s review the results in 3D to gain a better understanding. 
 [Zoom to Full Extent] from the bottom menu bar 
Visualizing the Results in 3D 
Most data objects within Visual MODFLOW Flex can be displayed in the 3D viewer, including 
model results such as head and drawdown values, and particle pathlines. Let’s review the 
results in 3D to gain a better understanding of the plume behaviour. 
Visual MODFLOW Exercise: Drumco – Part 2 
 
© Waterloo Hydrogeologic Page 19 
 Window / New 3D Window from the main menu 
A new 3D viewer window will open, called ‘3D Viewer – 1’. The viewer will be completely black 
since we do not currently have any data objects selected for display. Before we add any data 
objects, lets change the background colour of this scene. 
 Right-click anywhere in the 3D viewer 
 Background Color from the list that appears 
 Grey select grey as a background color 
 OK to accept and apply new background color 
We will now add some data objects to the scene. To start, we will add our basemap and 
pumping wells from the Data Tree. 
  DRUMCO from the Data Tree 
  Pumping_Wells from the Data Tree 
The 3D viewer will now show the basemap and pumping wells, as shown below: 
Visual MODFLOW Exercise: Drumco – Part 2 
 
© Waterloo Hydrogeologic Page 20 
 
We will now add the results of our MODFLOW-2005 and MODPATH run to this view, by 
selecting these objects from the Model Explorer. 
  Heads from the Model Explorer 
  Forward Pathlines from the Model Explorer 
The display will be dominated by the Heads object, since it’s currently showing a solid color in 
each and every model cell. Instead, we will display head values along a selected slice. 
 Right-click Heads from the Model Explorer 
 Settings from the list that appears 
 + Style to expand this branch of the settings tree 
 + Cells to expand this branch of the settings tree 
  Show Cells de-select, to deactivate cell view 
Visual MODFLOW Exercise: Drumco – Part 2 
 
© Waterloo Hydrogeologic Page 21 
 + Color Map to expand this branch of the settings tree 
  Show Color Map select, to activate color map 
 Layer from the Slice Type menu 
 Type: 6 in the Layer selection box 
 Type: 75 in the Transparency box 
 Isolines select this from the settings tree 
  Show Isolines select, to activate isolines 
 Layer from the Slice Type menu 
 Type: 6 in the Layer selection box 
  Contour Interval under the Line Properties frame 
 Type: 2.5 under Contour Interval 
 Type: 185 under Start Value 
 Type: 230 under Finish Value 
 Custom from the menu under Color 
 Black click the box next to Color and select black 
 Labels select this tab, next to Line Properties 
 Type: 1 under Number of Decimals 
 Color: Black click the Labels Color button and select black 
 Apply to apply all changes specified thus far 
 OK 
Let’s change the colour of our particle pathlines, to provide some contrast against other 
elements in the 3D Viewer. 
 Right-click Forward Pathlines from the Model Explorer 
 Settings from the list that appears 
 Blue clickthe box next to Color and select blue 
 Apply to apply all changes specified thus far 
 OK 
Your display should look like the image below: 
Visual MODFLOW Exercise: Drumco – Part 2 
 
© Waterloo Hydrogeologic Page 22 
 
Click and drag within the 3D viewer to reorient the viewer. The flexibility in viewing angles 
makes it easier to interpret your results. 
We’ll also display our model property Zone2, which is the zone corresponding to the pinched-
out aquitard. We’d like to apply a ‘slice’ to this zone, to display how thin this layer becomes in 
the area where the particles travel through it. 
 + Structure from the Model Explorer, to expand this folder 
 + Zones from the Model Explorer, to expand this folder 
  Zone2 from the Model Explorer 
 Right-click Zone2 from the Model Explorer 
 Settings from the list that appears 
 Color: Orange 
Visual MODFLOW Exercise: Drumco – Part 2 
 
© Waterloo Hydrogeologic Page 23 
 + Style to expand this branch of the settings tree 
  Transparent to make this zone transparent 
 Type: 50 under Transparency 
 OK 
Note: the property zone may not become transparent in 
some cases. This is related to the order that data objects 
have been added to the scene. If Zone 2 isn’t clearly 
transparent (with isolines visible throughout) please 
deactivate and reactivate the other data objects (i.e. 
DRUMCO site map, pumping wells, heads and pathlines). 
We’ll ‘slice’ away a portion of the data so that we can gain better insight into the relevant 
portion of the model (i.e. the area containing the plume). 
 Right-click anywhere in the 3D explorer 
 CutAway Properties from the list that appears 
  CutOffs Active to enable the cut offs 
  Active under the XZ Slice frame 
 Use the slider under XZ slice and scroll until the Fraction field says 0.3 
 OK 
This will remove all data from the 3D viewer on the ‘lower’ portion of the model domain (i.e. 
approximately from Y=0 to Y=1000m. Let’s retain the particle pathlines within the cutaway 
region: 
 Right-click Forward Pathlines from the Model Explorer 
 Settings from the list that appears 
 + Style to expand this branch of the settings tree 
  Show in Cutaway region to display the particles in the cutaway region 
 OK 
Your display should look like the first image on the next page. You can reorient the 3D viewer so 
that you’re viewing the scene from the South-West corner (along the cutaway region) and apply 
a vertical exaggeration to recreate the 2nd image on the next page. 
As you can see, each data object has a wide variety of settings which can be utilized to 
customize the viewers as the situation requires. Only a small sampling of the available settings 
has been touched upon here. Take a few additional minutes to explore additional settings and 
options. 
Now is a good time to save the project. 
 File / Save 
OR 
Visual MODFLOW Exercise: Drumco – Part 2 
 
© Waterloo Hydrogeologic Page 24 
 from the main toolbar 
 
 
Visual MODFLOW Exercise: Drumco – Part 2 
 
© Waterloo Hydrogeologic Page 25 
PART 3: REMEDIAL FEASIBILITY AND DESIGN – PUMP AND TREAT SYSTEM 
The first remedial option to be evaluated is a single-well pump-and-treat system to capture the 
groundwater plume, preventing further migration and removing it for treatment. The 
objectives of the exercise are: 
• Utilize backward tracking particles to determine the area of influence, or capture zone, 
for a pumping well operating at a specified rate 
• Determine the optimal pumping rate for a single well that maximizes the operational 
effectiveness of the system by capturing and removing the entire groundwater plume; 
Design Objectives 
The design process of a pump-and-treat remediation system focuses on the maximization of 
both the operational effectiveness and the efficiency of the remediation system, while 
simultaneously meeting clean-up targets. 
A Visual MODFLOW flow and contaminant transport model can be a very powerful tool. These 
models are commonly used by remediation engineers during the initial feasibility study stage of 
remedial alternative selection, and later in the design process of groundwater remediation 
systems. The model enables you to develop an initial system design to meet operational goals 
and clean-up targets. The model also enables you to explore cause-and-effect scenarios to 
assess remediation system sensitivity to local geologic and hydrologic extremes. 
In this exercise, you will use particles to represent the extent of a groundwater contaminant 
plume. We use particles in this exercise because of time constraints, since running an actual 
contaminant transport simulation could require an hour or more to complete. If this were an 
actual project, you could use real contaminant concentrations measured in monitoring wells at 
the site for the simulation. You will design the system to hydrodynamically capture and remove 
all the contaminant particles in the groundwater with the interceptor well, while trying to 
minimize the amount of clean water removed for treatment. 
Before you proceed, you must ensure that you are viewing the appropriate modelling 
workflow. At this point we have completed a conceptual model and a single numerical model 
(base case) of the project site. In order to preserve out initial results for later review, we will 
simply clone our initial numerical model and then add our pumping well and backward particles 
to the cloned model. 
 Right-click ‘Run’ under the NumericalGrid branch of the Model Explorer 
 Clone Model Run… to clone this model run and associated inputs 
Visual MODFLOW Exercise: Drumco – Part 2 
 
© Waterloo Hydrogeologic Page 26 
 
Cloning a model run duplicates all inputs associated with the original model run. You can then 
make a few small changes and re-translate and run the model. This is a great way of saving time 
if you need to evaluate several variations of the same model. 
After cloning your model run you will notice that a new branch has appeared in the Model 
Explorer, under NumericalGrid. The new model run has been labelled ‘Run1’. You need to load 
the numerical workflow for this new run. 
 Right-click Run1 under the NumericalGrid branch of the Model Explorer 
 Open Related Workflow(s)… from the menu that appears 
The numerical workflow associated with Run1 will open, and a new tab will become active. You 
will now proceed to revise the inputs for this new model run, adding a pumping well and 
backward tracking particles. 
Assigning the Pumping Well 
To assign a new pumping well you must return to the Define Boundary Conditions step in the 
numerical modelling workflow. 
 Define Boundary Conditions click this workflow step directly from the workflow 
 navigator 
  DRUMCO from the Data Tree, to help you place the well 
 Set background color to grey 
 Deactivate any unnecessary data objects (i.e. Recharge, River and Constant Head BCs) 
Visual MODFLOW Exercise: Drumco – Part 2 
 
© Waterloo Hydrogeologic Page 27 
 [Zoom to Box] zoom around the area of the Drum Disposal Area 
 Layer: 2 ensure that you are viewing model Layer 2 
 Wells select this type of boundary condition from the first 
 dropdown list under the Toolbox 
 Assign > Wells under Toolbox 
 Click once on Row 44, Column 24 
 Finish 
  Create a new numerical well group from the window that appears 
 OK 
 Well Object Name: RW-1 
 Name (under Well Heads table): RW-1 
 X = 1575 
 Y = 1825 
 End Time (day) = 3650 
 Rate (GPM) = -10 
 OK 
Note: the pumping rate must be a negative value to 
establish an extraction well. A positive pumping rate would 
indicate an injection well. 
Before clicking OK and creating the pumping well, the Create Well Boundary Condition window 
will look like the image below: 
 
The screened interval for RW-1 has been restricted to Layer 2, which is the lower model layer in 
Visual MODFLOW Exercise: Drumco– Part 2 
 
© Waterloo Hydrogeologic Page 28 
the Upper Aquifer. This approach will help to minimize problems associated with drying of cells 
at the pumping well. Specifically, as MODFLOW 2005 attempts to find a solution, it will 
iteratively assign heads at all cells, including the cells representing the pumping well. If the head 
falls below the bottom of a cell that represents the pumping well, the cell is automatically 
turned off and the pumping rate is decreased proportionately. If the pumping well only spans a 
single cell then when that cell is turned off the pumping rate would go to zero. 
A pink well symbol will appear at the leading edge of the groundwater plume indicating the 
location of the interceptor well, which will prevent further migration and achieve plume 
capture. We will now assign backward tracking particles to this well, to ensure that the capture 
zone is large enough. 
Assigning Particles 
The forward particles that were assigned previously will be used to determine if the water 
flowing through the contaminated area will be captured by the interception well. Another 
aspect of interception well design is to minimize the amount of uncontaminated water that is 
being collected. This can be assessed by assigning backward-tracking particles in a circle around 
the well. These particles will also help to delineate the capture zone of that well. If the capture 
zone is significantly larger than the contaminated zone, the design should be modified e.g. 
lower pumping rate, more wells, etc. 
To assign particles we must move to the Define Particles workflow step: 
 Define Particles click this workflow step directly from the workflow 
 navigator 
  RW-1 from the Model Explorer, so that the well will be 
 visible 
 Zoom so that you can clearly see the new well 
 Assign > Circle… to assign a circle of particles 
 Click RW-1 
 Assign to Layer: 2 
 Radius: 10 
 # Particles: 10 
 Particle Type: Backward 
 OK 
A circle of backward tracking particles has now been assigned to layer 2. If you view layer 2 in 
the Flex viewer you will see that RW-1 is now ringed by a group of red circles, representing the 
backward tracking particles. 
Translate and Run the Pump-and-Treat Remediation Simulation 
You will now run the revised model with the additional pumping well. When you cloned the 
original model run all translation settings were retained, but we will need to make some 
Visual MODFLOW Exercise: Drumco – Part 2 
 
© Waterloo Hydrogeologic Page 29 
changes for this model run to converge successfully, specifically the rewetting options. 
During the simulation calculations, some of the model cells may go dry from pumping the 
remediation well. Visual MODFLOW allows you to specify rewetting of the dry cells as the water 
table fluctuates during the simulation calculations. To specify the rewetting option: 
 Translate click this workflow step directly from the workflow 
 navigator 
 Rewetting select this node in the settings tree 
 Wetting threshold (WETDRY) value: 0.25 
 Iteration interval for attempting to wet cells: 3 
The rewetting translation settings should appear exactly as shown in the image below: 
 
The controlling cell, or cell that determines when a dry cell is to be rewetted, can be specified 
using the ‘Wetting method (WETDRY) flag’ setting. Two options are available: 
1. From below (WETDRY < 0); or 
2. From sides and below (WETDRY > 0) 
The Wetting head (IHDWET) can be calculated from neighboring cells or from a user-specified 
threshold. The Wetting threshold is used to determine whether a cell will be rewetted. For 
example, if a dry cell has a bottom elevation of 10 and the Wetting threshold is set to 0.25, the 
dry cell will be rewetted when the elevation in the controlling cell reaches 10.25. The trial head 
in the dry cell is calculated by one of two methods: 
i) Head Calculated from neighbours 
Head = Zbot + Cell wetting factor (Neighboring head - Zbot) 
ii) Head Calculated from threshold 
Head = Zbot + Cell wetting factor (Wetting threshold) 
Note that the Cell wetting factor is used in both equations. The following schematic diagram 
Visual MODFLOW Exercise: Drumco – Part 2 
 
© Waterloo Hydrogeologic Page 30 
illustrates these concepts. 
 
 
 
 
 
 
 
 
 
Finally, by specifying a wetting interval of 3 iterations, we have instructed MODFLOW 2005 to 
rewet cells every third outer iteration. 
You’re now ready to translate and run the new iteration of the model, this time with a new 
pumping well and backward tracking particles. 
 to translate input files 
 (Next Step) from the workflow navigator panel 
 to run the model engines 
Displaying the Pump and Treat Simulation Results 
You can now analyse the results of your pump and treat system. 
 (Next Step) from the workflow navigator panel 
 View Maps 
A 2D viewer will be visible, displaying the Heads results from the completed model run. Your 
display should look like the image below (note the dry cells near the middle of the model 
domain: 
Zbot 
Wet/dry threshold 
Neighboring cell 
Dry cell 
The dry cell will be 
rewetted under this 
scenario. 
The dry cell will not be 
rewetted under this 
scenario. 
Visual MODFLOW Exercise: Drumco – Part 2 
 
© Waterloo Hydrogeologic Page 31 
 
We’ll make several small visualization changes to help us view the results. First review the 
results in layer view: 
  Layer: 1 to ensure Layer view is active 
 Set background color to grey 
 to remove gridlines from the view 
  DRUMCO from the Data Tree 
  Forward Pathlines from the Model Explorer 
  Backward Pathlines from the Model Explorer 
 [Zoom to Box] zoom around the area of the Drum Disposal Area 
Your display should look something like the image below: 
Visual MODFLOW Exercise: Drumco – Part 2 
 
© Waterloo Hydrogeologic Page 32 
 
You can also review the results in column view: 
  Column: 24 ensure Column view is selected (Column 24) 
  Layer: 1 ensure Layer view is deactivated 
 Zoom 
Your display should look something like the image below (column view): 
Visual MODFLOW Exercise: Drumco – Part 2 
 
© Waterloo Hydrogeologic Page 33 
 
Visual MODFLOW enables you to quickly visualize effects of your design. In this case, the 
pumping well captures only a portion of the groundwater plume. You can visualize the results 
of the model in 3D by following the guidelines in the next section. 
Using a follow-up, iterative process of relocating the well or changing the pumping rate or both, 
also try to determine the optimum operational design to capture the groundwater plume and 
remove the minimum amount of uncontaminated water. 
Visualizing 3D Pump and Treat Simulation Results 
To visualize the results in 3D, open a new 3D window from the main menu. The results from the 
Visual MODFLOW Exercise: Drumco – Part 2 
 
© Waterloo Hydrogeologic Page 34 
most recent model run can be visualized along with the data objects used to generate the 
model. As you are already familiar with the operational controls of 3D Explorer, you should be 
able to visualize the pump-and-treat results fairly quickly. 
By experimenting with these options, you will quickly be able to manipulate the model domain 
to the desired viewpoint. Depending on your orientation, your display may appear similar to 
the following figure: 
 
As you can see the pump-and-treat well does not capture all of the particles destined for the 
water supply well. The remediation well does capture the middle portion of the contaminant 
plume, but several particles on the edges of the plume skirt around the remediation well. If you 
have time after completing the Drumco exercise, come back to this part of the exercise and re-
design the pumping well with a higher pumping rate, or place additional wells to capture the 
plume. Once completed, re-open the 3D Explorer to quickly visualize the 3Dresults. 
Increasing the Pumping Rate for Full Capture 
Now, try increasing the pumping rate to achieve full capture of the contaminated zone. You can 
experiment with this in two stages to see how pumping rate increases affect the size of the 
Visual MODFLOW Exercise: Drumco – Part 2 
 
© Waterloo Hydrogeologic Page 35 
capture zone. Rather than duplicating model runs for each iteration of this model you can 
simply increase the pumping rate for the existing numerical model by right-clicking RW-1 from 
the Model Explorer (under Model Run1) and making the required changes to the pumping rate. 
Then re-translate and re-run the model and review the resulting pathlines/drawdown. 
You can attempt to find the ideal pumping rate in two stages: 
Stage 1: Q = 20 gpm 
Stage 2: Q = 25 gpm 
A pumping rate of 20 gpm should yield complete capture, as seen in the figure below. Note the 
presence of dry cells, denoted by the olive-green cells. Also note that the far-left particle lies 
outside the original extent of the plume, so we can overlook this stray pathline: 
 
And, 25 gpm yields full capture, along with an especially pronounced dry zone: 
Visual MODFLOW Exercise: Drumco – Part 2 
 
© Waterloo Hydrogeologic Page 36 
 
If you wish, you can also experiment with more than one well. Using multiple wells in an 
interception system is generally advisable because it allows the system to continue functioning 
if one of the pumps breaks down or when the wells require maintenance. 
Now is a good time to save the project. 
 File / Save 
OR 
 from the main toolbar 
 
 
Visual MODFLOW Exercise: Drumco – Part 2 
 
© Waterloo Hydrogeologic Page 37 
PART 4: MINIMIZING PUMPING WITH A BARRIER WALL AND COVER 
One of the problems with conventional pump-and-treat systems is the large volume of slightly 
contaminated water that is collected. Often the concentrations are too low to treat properly, 
and the large volumes are difficult to handle. One way to deal with this is to install a low-
permeability wall around the contaminated area to contain the contamination, and a low 
permeability cover to minimize the amount of recharge. We will simulate this approach using 
the “horizontal flow barrier” option that is incorporated into MODFLOW 2005. 
Before assigning the barrier wall, we will once again clone our model run so that we don’t 
overwrite any of our previous results. 
 Right-click Run1 under the NumericalGrid branch of the Model Explorer 
 Clone Model Run… to clone this model run and associated inputs 
 Right-click Run2 under the NumericalGrid branch of the Model Explorer 
 Open Related Workflow(s)… from the menu that appears 
Once completed, turn OFF/DELETE the pumping well (RW-1) that you assigned earlier. 
 Define Boundary Conditions click this workflow step directly from the workflow 
 navigator 
 Wells select this boundary condition type from the list 
 under Toolbox 
 Erase > Group from the Toolbox 
 Click RW-1 in the Flex viewer, to select this well for deletion 
 Yes to confirm that RW-1 will be deleted 
We will also delete the circle of particles which we had placed around this well. 
 Define Particles click this workflow step directly from the workflow 
 navigator 
 Layer: 2 ensure you are viewing model layer 2 
 Delete > Current Layer from the Toolbox 
All particles within the currently viewed layer (i.e. layer 2) will be deleted. 
Once completed, we can begin adding the barrier wall to the model domain. The barrier wall 
will be assigned around the contaminated area, for reducing the flow of groundwater 
horizontally through the source of contamination. 
To assign a barrier wall, we will use the Wall (HFB) package. You are going to assign a barrier 
wall as shown in the image below. The numbers shown are the row and column at each corner. 
Instructions are given below. When digitizing the barrier wall, check that rows and columns are 
consistent. Also, no overhang is needed on the wall. 
Visual MODFLOW Exercise: Drumco – Part 2 
 
© Waterloo Hydrogeologic Page 38 
However, wall boundary conditions can only be assigned in Visual MODFLOW Flex using an 
existing data object. For this reason, we will first have to draw a polygon which delineates the 
extent of the wall boundary condition. 
 
Before proceeding we need to generate the polyline data objects (four of them) which will be 
used to define the wall. 
 Right-click in the Data Tree 
 Create New Data Object… from the menu that appears 
A new window called ‘Create New Data Object’ will open. 
 Data Type = Polyline 
 Data Name: Wall1 type this value for Data Name 
Repeat these steps until you have four polyline objects, named Wall1, Wall2, Wall3 and Wall4 
At this point we need to visualize the drum disposal area so that we can properly draw our 
polygon. We’ll turn on the DRUMCO site map object and the Recharge 1 boundary condition. 
The site map will help us to contextualize the new object. The recharge boundary condition is 
activated to help us to envision the spacing of cells. Unfortunately it isn’t possible to visualize 
Visual MODFLOW Exercise: Drumco – Part 2 
 
© Waterloo Hydrogeologic Page 39 
the numerical grid in a 2D viewer, so we can visualize the recharge boundary condition as a 
work-around. 
 Window > New 2D Window from the main menu 
 Background color: white 
  DRUMCO from the Data Tree 
  Recharge 1 from the Model Explorer, under Run2 
 [Zoom to Box] zoom around the area of the Drum Disposal Area 
Your display should look something like the image below: 
 
Now you will activate the newly created Wall1 object, and use the drawing tools to create the 
data object. Wall1 will represent the northern boundary of the walled off area (i.e. from 
row/column 16,17 to 17,27). 
  Wall1 activate this object in the Data Tree 
Visual MODFLOW Exercise: Drumco – Part 2 
 
© Waterloo Hydrogeologic Page 40 
Note: the currently selected data object is shown at the 
bottom left of the 2D viewer, next to the ‘Layer’ field. Only 
the currently selected data object can be edited. 
 [Pick Mode] enable pick mode by clicking the button in the toolbar 
 [Begin edit] to begin ‘Edit’ mode 
 [Add polyline] to add a polygon to this data object 
 Draw the polyline: left-click to start and double-click to end 
o The line will extend from the first coordinate below to the 2nd 
▪ X1,Y1 = 965, 3135 
▪ X2,Y2 = 1850, 3135 
 [End Edit] to end edit and accept changes to data object 
You will now repeat these steps for Wall2, Wall3 and Wall4, using the approximate start/end 
coordinates listed below: 
• Wall2: X1,Y1 = 965, 1765; X2,Y2 = 1915, 1765 
• Wall3: X1,Y1 = 965, 3135; X2,Y2 = 965, 1765 
• Wall4: X1,Y1 = 1915, 3135; X2,Y2 = 1915, 1765 
Note: you can correct these data objects after creating 
them by right-clicking the data object in the Data Tree and 
selecting ‘View Spreadsheet’ from the menu that appears. 
Use the [Begin edit] button to enable editing of the 
spreadsheet/table that appears. When you’ve finished 
correcting the values, you can click the [End Edit] 
button to finalize the edits. 
After creating these four polylines they should form a rectangle. Don’t worry about exact 
placement of the lines; they will be assigned to the nearest cell face when they are assigned as 
wall boundaries. If you activate all four walls in a 2D viewer you should see something close to 
the image below: 
Visual MODFLOW Exercise: Drumco – Part 2 
 
© Waterloo Hydrogeologic Page 41 
 
You can now close the 2D viewer and return to the new numerical workflow (NumericalGrid-
Run2). 
 [X] to close 2D viewer tab 
 NumericalGrid-Run2 select this tab 
Now, return to the Define Boundary Conditions step so we can define the wall using our newly 
created polygon: 
 Define Boundary Conditions click this workflow step directly from the workflow 
 navigator 
 Layer: 1 ensure you are viewing modellayer 1 
 Wall(HFB) select this boundary condition type from the list 
 shown under the Toolbox 
 Assign 
A window (Define Wall Boundary Condition) will open, as shown below: 
Visual MODFLOW Exercise: Drumco – Part 2 
 
© Waterloo Hydrogeologic Page 42 
 
The wall boundary condition is assigned using a polyline to delineate the horizontal extents of 
the wall and two horizons to delineate the vertical extents of the wall. Select Wall1 as the 
polyline and use ground and Surface2 as the required horizons. 
 Type: Wall1 in the Name field 
 Wall1 select this data object from the Data Tree 
 [Select Polyline] to use this object 
 ground select this data object from the Data Tree 
 [Top Horizon] to use this object 
 Surface2 select this data object from the Data Tree 
 [Bottom Horizon] to use this object 
 Type: 1e-7 for Conductivity (cm/s) 
 Type: 3 for Thickness (ft) 
The window should now look like the image below: 
Visual MODFLOW Exercise: Drumco – Part 2 
 
© Waterloo Hydrogeologic Page 43 
 
 OK to accept values and create Wall 
Now repeat these steps for the remaining walls. The same conductivity and thickness values, 
and the same surfaces (i.e. ground and Surface2) can be used for the remaining walls. When 
you’re finished, your display should look like the image below: 
Visual MODFLOW Exercise: Drumco – Part 2 
 
© Waterloo Hydrogeologic Page 44 
 
To minimize problems with numerical instability and to find the optimum pumping rate more 
quickly, you are going to simulate a pumping well in the middle of the enclosure with a constant 
head cell. The following steps will guide you through the process of assigning a head and a 
ZoneBudget zone. 
ZoneBudget is a utility program that is executed after the MODFLOW-2005 simulation is 
complete. It calculates a mass balance for user defined flow zones. The following instructions 
will lead you through the appropriate steps. A head of 214 ft at the pumping well will probably 
ensure an inward gradient into the enclosure. Ensure you are still on the Define Boundary 
Condition step (Run2) and viewing layer 1, and then assign a constant head boundary 
condition: 
  Layer: 1 ensure Layer view is activated 
 Constant Head from the list of available boundaries under Toolbox 
 Assign > Cells from the Toolbox 
 Click once on Row 32, Column 22 
 Finish 
The Define Boundary Condition window will appear. 
Visual MODFLOW Exercise: Drumco – Part 2 
 
© Waterloo Hydrogeologic Page 45 
 OK to accept the default values 
 Type: 214 under the Starting Head (ft) field 
 Type: 214 under the Ending Head (ft) field 
 Finish 
Note that the constant head cell has been automatically placed in Layer 2, based on the head 
values entered (which fall below the bottom of layer 1). Your display should look like the image 
below (for layer 2): 
 
Now that a Constant Head cell has been assigned to simulate the well, a ZoneBudget zone 
needs to be assigned so that the flow out of the model through the constant head can be 
determined. This flow rate would be the design flow for the well. 
 Define Zone Budget Zones click this workflow step from the workflow navigator 
  Layer: 2 ensure you are viewing Layer 2 
Visual MODFLOW Exercise: Drumco – Part 2 
 
© Waterloo Hydrogeologic Page 46 
  Constant Head 2 ensure the new constant head boundary is visible 
 Assign > Single from the Toolbox 
 Click the cell with Constant Head 2 
 Finish 
The Create New Zone Budget Zone window will open. It should look like the image below: 
 
 New to assign this cell to a zone of it’s own 
 OK to create the new zone 
Now, we will add a circle of backward tracking particles to this location. To do so, 
 Define Particles click this workflow step from the workflow navigator 
  Zone Budget activate Zone Budget view 
  Layer: 2 ensure you are viewing Layer 2 
 Assign > Circle 
 Click once on the blue cell (i.e. the Zone Budget cell) 
 OK to accept default values and create particles 
Now we will assign a lower recharge rate within the walled area to simulate a low-permeability 
cover. The purpose of this cover is to reduce the pumping rate and therefore treatment costs. 
 Define Boundary Conditions click this workflow step from the workflow navigator 
If you are not already viewing Layer 1, change to this view because recharge rates can be assigned 
only when viewing Layer 1. 
Visual MODFLOW Exercise: Drumco – Part 2 
 
© Waterloo Hydrogeologic Page 47 
  Layer: 1 ensure you are viewing Layer 1 
 Recharge from the list of available boundaries under Toolbox 
 Assign > Polygon to begin drawing a polygon 
 Draw a rectangle which covers the entire walled area (left-click to begin drawing, then right-
click and select Finish after drawing the rectangle) 
The Define Boundary Condition window will open. 
 Next >>> to accept the default values in the first window 
 Schedule: Static change from Transient to Static 
 Type: 2 under Recharge (in/yr) 
 (or F2) to assign this value to the entire 
 column 
 Type: 0 under Ponding (ft) 
 (or F2) to assign this value to the entire 
 column 
 Finish 
When you’re finished the recharge zones (Layer 1) should look like the image below: 
 
You’re now ready to run the updated model with our flow barrier. 
Visual MODFLOW Exercise: Drumco – Part 2 
 
© Waterloo Hydrogeologic Page 48 
 Single Run click this workflow step directly from the workflow 
 navigator 
Make sure that MODFLOW-2005, MODPATH and ZoneBudget are all selected in the single 
engines workflow step. 
  ZONEBUDGET ensure that Zone Budget is selected and active 
  MODPATH ensure that MODPATH is selected and active 
 (Next Step) from the workflow navigator panel 
 to translate input files 
 (Next Step) from the workflow navigator panel 
 to run the model engines 
The MODFLOW-2005 model should run in a few moments, quickly followed by the ZoneBudget 
and MODPATH engines. The entire model run should take no more than 1 minute to run. 
 (Next Step) from the workflow navigator panel 
 View Maps 
By default, the resulting heads for Layer 1 of your model will be displayed. Turn off gridlines by 
clicking the button in the toolbar ( ), display the backward pathlines in blue and change the 
colour of the walls to purple. Your display should look like the image below. 
Visual MODFLOW Exercise: Drumco – Part 2 
 
© Waterloo Hydrogeologic Page 49 
 
Note that the particle traces indicate that some flow is induced through the barrier wall. This flow 
is caused by the strong gradient across the northern wall as a result of reducing the water table 
elevation inside the enclosure (also note that layer 1 has gone dry within the enclosure). An 
independent ZoneBudget analysis indicates the following sources of water into the enclosure: 
• 60% from flow through the wall 
• 40% from recharge through the low-permeability cover 
A low water level was specified inside the enclosure to help ensure that an inward gradient would 
be maintained at the south end of the enclosure. Because the regional water table slopes 
southward, this results in a large gradient across the northern wall. 
The following image displays the resulting heads/pathlines as a cross-section view through 
column 24 (vertical exaggeration of 20, gridlines turned on). As you can see, the gradient through 
the northern wall is great enough to force particles under the barrier wall: 
Visual MODFLOW Exercise: Drumco – Part 2 
 
© Waterloo Hydrogeologic Page 50 
 
Now you can use Zone Budget to determine the pumping rate that would be required to produce 
the pumping level specified at the constant head cell. 
 View Charts click this workflow step from the workflow navigator 
By default, the View Charts workflow step will display the calculated vs observed head values for 
the model, as shown in the image below:Visual MODFLOW Exercise: Drumco – Part 2 
 
© Waterloo Hydrogeologic Page 51 
 
You can load the results of our ZoneBudget analysis by clicking the Zone Budget button at the 
top-left (highlighted in the image above). Clicking that button will load a new Zone Budget 
window, displaying the mass balance information for the previously defined Zone Budget zones. 
Please note that you can click the Mass Balance button to open a similar window which displays 
the overall mass balance of your entire model domain (similar to Zone Budget, except the entire 
model represents a single ‘zone’). 
 Zone Budget click this button at the top-left of the View Charts 
 window 
A window will open with four separate graphs displays (i.e. Time step, Time Series, IN-OUT and 
Percent Discrepancy). Click the Time step graph to bring it to the front. Your display will look like 
the image below (you can click any data point to display details): 
 Time step click this graph to bring it to the front 
Visual MODFLOW Exercise: Drumco – Part 2 
 
© Waterloo Hydrogeologic Page 52 
 
The time step graph displays the inflow and outflow rates for each user-defined zone at time-
step (there is only one output time for this model, since it’s steady-state). Ensure that you are 
viewing the results from Zone 2, which was the zone we set for the constant head cell within our 
enclosure. Note the flow rate for Constant Head in Zone 2. A value of approximately 1,272 ft3/day 
will be displayed, as shown in the figure. This flow rate is equivalent to 6.6 gallons/minute, and 
represents the flow rate leaving the model through the constant head cell. These results indicate 
that the pumping rate can be significantly reduced by surrounding the contamination with a 
barrier wall and covering it with a low-permeability cover, even though some flow is induced 
through the wall. 
The next remediation strategy to test will be an interceptor trench placed downgradient from 
the contaminant plume. 
 Close the Zone Budget window click the red X at the top-right corner of window 
Now is a good time to save the project. 
 File / Save or from the main toolbar 
 
Visual MODFLOW Exercise: Drumco – Part 2 
 
© Waterloo Hydrogeologic Page 53 
PART 5: REMEDIAL FEASIBILITY AND DESIGN – INTERCEPTOR TRENCH 
The third remedial alternative you will evaluate is an interceptor trench used to capture the 
groundwater plume to prevent further migration. In the model, you will simulate the interceptor 
trench with a special model component known as a “drain”. In the context of MODFLOW, drains 
will remove water from the aquifer at a rate proportional to the difference between the head in 
the aquifer and a fixed head/elevation (e.g. the elevation of the drain). It is assumed that the 
drain has no effect if the head in the aquifer falls below the fixed head of the drain. 
Design Objectives 
As a remedial alternative, the interceptor trench is analogous to the pump-and-treat system you 
assessed in Part 2. However, instead of using a pumping well to capture the contaminant plume, 
a trench is installed to capture the contaminated water. Water that accumulates in the trench is 
then removed by pumping for treatment off-site. Occasionally, additional remediation measures 
such as air-sparging are installed in such trenches. 
In this exercise, you will determine the optimum design depth and length of the trench so it 
intercepts all of the contaminated particles. The ZoneBudget utility will again be used, this time 
to quickly determine inflow and outflow rates of your trench. Consequently, these data can be 
used to properly size a lift station to remove contaminated water from the trench and estimate 
the required treatment capacity of your system. 
Because your Visual MODFLOW model is a three-dimensional model, it will simulate vertical flow 
gradients and the effects of heterogeneous geologic deposits on the migration of the 
contaminant plume. This allows you to account for these important influencing features of the 
groundwater flow system in your design. Simple two-dimensional analytical equations, 
occasionally used in the design of remedial systems, do not account for these vertical flow 
components and heterogeneous geology — and often result in systems that are seriously over or 
under-designed. 
Assigning the Trench and Zone Budget Zones 
Before we begin assigning new model components, we will clone our initial model run. That way 
we can retain the previous simulation results, with our barrier walls. 
 Right-click Run under the NumericalGrid branch of the Model Explorer 
 Clone Model Run… to clone this model run and associated inputs 
 Right-click Run3 under the NumericalGrid branch of the Model Explorer 
 Open Related Workflow(s)… from the menu that appears 
To begin assigning the trench (drain) remediation system: 
 Define Boundary Conditions click this workflow step from the workflow navigator 
 Change background colour to white 
Visual MODFLOW Exercise: Drumco – Part 2 
 
© Waterloo Hydrogeologic Page 54 
 [Zoom to Box] zoom around the area of the Drum Disposal Area 
 Drain select this boundary condition from the menu under 
 Toolbox 
 Assign > Polyline button under the Toolbox 
 Left-click once on Row 44, Column 20 
 Right-click once on Row 44, Column 31 
 Click Finish from the menu that appears 
The Define Boundary Condition window will open. After clicking past the first step and entering 
data, the Define Boundary Condition window will look like the image below: 
 Next >>> to proceed to the next step in defining the boundary 
 condition 
 Type: 214 in the Drain Elevation field 
 (or F2) to assign this value to the entire 
 column 
 [Use Default Conductance] to specify conductance, rather than calculate based on 
 other inputs 
Note: if the ‘Use default conductance’ option is turned off, 
the fields used for calculating the Drain Conductance value 
(Conductance per unit length or area) are removed from 
the table and the Conductance field becomes a read/write 
field where any value may be entered. See the user manual 
for more information 
 
 Type: 1500 in the Conductance field 
 (or F2) to assign this value to the entire 
 column 
 
Visual MODFLOW Exercise: Drumco – Part 2 
 
© Waterloo Hydrogeologic Page 55 
 Finish to finalize inputs and create drain 
The Conductance value is inversely proportional to the resistance to flow between the aquifer 
and the drain. In this example, an artificially high conductance value was specified to simulate a 
hydraulic connection with little flow resistance between the aquifer and the drain. 
Please note that the drain boundary condition will be automatically placed in Layer 2, based on 
the specified drain elevation. When you’re finished, view Layer 2 and you should see something 
like the image below: 
 
Visual MODFLOW Exercise: Drumco – Part 2 
 
© Waterloo Hydrogeologic Page 56 
We would also like to assign the drain cells to a zone budget zone. Proceed to the Define Zone 
Budget Zones workflow step and assign the required cells to a new zone: 
 Define Zone Budget Zones click this workflow step from the workflow navigator 
  Drains turn on the drains to help you find the required cells 
  Layer: 2 ensure that you are viewing model Layer 2 
 Zoom to the Drum Disposal Area 
 Assign > Polyline click the button under the Toolbox 
 Left-click once to start line, right-click and select Finish to finish line 
 Draw a line across all the cells which include the drain boundary 
A Create New Zone Budget Zone window will open. 
 New click this button to assign the cells to a new zone 
 OK to accept the remaining settings and create new zone 
Translate and Run 
You will now translate and run the updated model. 
 Single Run click this workflow step directly from the workflow 
 navigator 
Make sure that MODFLOW-2005, MODPATH and ZoneBudget are allselected in the single 
engines workflow step. 
  ZONEBUDGET ensure that Zone Budget is selected and active 
  MODPATH ensure that MODPATH is selected and active 
 (Next Step) from the workflow navigator panel 
 to translate input files 
 (Next Step) from the workflow navigator panel 
 to run the model engines 
The MODFLOW-2005 model should run in a few moments, quickly followed by the ZoneBudget 
and MODPATH engines. The entire model run should take no more than 1 minute to run. 
 (Next Step) from the workflow navigator panel 
 View Maps 
Visual MODFLOW Exercise: Drumco – Part 2 
 
© Waterloo Hydrogeologic Page 57 
Displaying the Trench and Drain Simulation Results – 2D 
The results of the model should look like the image below (viewing Layer 2, gridlines turned off, 
forward pathlines activated, drain activated/visible): 
 
From this display you can see that the trench remediation system completely captures the 
groundwater plume, as none of the particles from the drum disposal area are escaping. 
Now that you have determined the trench system will effectively capture the groundwater 
plume, you will need to determine the extraction rate required to remove the contaminated 
water from the trench. This flow rate information will help you to size the required pumps, and 
the effluent treatment system. Visual MODFLOW creates a listing of the flows into and out of 
each of the boundary conditions specified in the model. 
 View Charts click this workflow step directly from the workflow 
 navigator 
 Mass Balance click the button at the top-left corner of the View 
Visual MODFLOW Exercise: Drumco – Part 2 
 
© Waterloo Hydrogeologic Page 58 
 Charts interface 
 Time step ensure you are viewing the Time step graph 
 Zone 2 ensure you are viewing results for Zone 2 
Your display should look something like the image below: 
 
The Mass Balance graphs give you a summary of the flows IN and OUT of the aquifer for each type 
of sink or source defined in the model. A sink is something that removes water from the model 
system, while a source is something that provides water to the model system. Pumping wells and 
drains are examples of sinks, and recharge areas are examples of sources. A river boundary can act 
as a sink or a source, depending on the head in the aquifer relative to the river stage elevation. 
Please note that you can also review Zone Budget graphs, which are very similar to Mass Balance 
graphs. The difference is that the Zone Budget graphs provide a mass balance analysis for each user 
defined zone, instead of a mass balance on the entire model domain. 
As illustrated above, the flow rate out of the drains is approximately 8,519 ft3/day. The units for 
the flow rate in this display are derived from the units of length and time that are defined for the 
model, regardless of the units defined for flow in Visual MODFLOW. This equates to an average 
flow rate of approximately 44 US gallons per minute. 
Visual MODFLOW Exercise: Drumco – Part 2 
 
© Waterloo Hydrogeologic Page 59 
 Close the Mass Balance window click the red X at the top-right corner of window 
Displaying the Trench and Drain Simulation Results – 3D 
Take a few minutes to visualize the results of the trench and drain model in 3D. Open a new 3D 
window and add the following data objects from Run3: 
• Outputs 
o Water Table 
o Forward Pathlines 
• Inputs 
o Drain 1 
o Zone 2 (i.e. the structural zone; found in the Model Explorer under 
‘Structure>Horizons’) 
Take a few minutes to see if you can recreate this 3D view on your own computer. 
 
Visual MODFLOW Exercise: Drumco – Part 2 
 
© Waterloo Hydrogeologic Page 60 
Save the current scene by right-clicking and selecting ‘Save As Image’. 
 Right-click anywhere in the 3D scene window 
 Save As Image from the list/menu that appears 
The following Save as Image window will open: 
 
The save the image simply select an image size, browse to the location where you’d like to save the 
image (by pressing the […] button), provide a file name and click OK. 
You can also save scene parameters (i.e. orientation of the view, background color, etc.) for later 
use by right-clicking and selecting ‘Save scene params’. This is helpful if you find a particular 
viewing angle that you like; save those scene parameters and then change the view. The saved 
view can be achieved again by right-clicking and selecting ‘Load scene params’. 
Testing a Shallower Drain 
Before testing our final remediation system (funnel and gate), you will test one final design of the 
trench. The current trench design does a good job of capturing the plume, but it also generates 
quite a lot of water. You can try to increase the drain elevation to reduce the volume of water 
generated. We’ll see if increasing the elevation continues to provide full plume capture. 
 Ensure you are viewing the NumericalGrid-Run3 workflow 
o Click the correct tab or right-click Run3 from the Model Explorer and select ‘Open 
Related Workflow(s)’ 
 Define Boundary Conditions click this workflow step directly from the workflow 
 navigator 
  Layer: 2 ensure that you are viewing model Layer 2 
 Drain select this boundary condition from the menu under 
 the Toolbox 
 Erase > Group 
 Click the trench clicking any cell containing the existing drain will delete 
 the group 
Visual MODFLOW Exercise: Drumco – Part 2 
 
© Waterloo Hydrogeologic Page 61 
 Yes to accept warning and delete the drains 
  Layer: 1 ensure that you are viewing model Layer 1 
 Assign > Polyline 
 Left-click once on Row 44, Column 20 
 Right-click once on Row 44, Column 31 
 Click Finish from the menu that appears 
The Edit Boundary Condition window will open. Click Next >> to accept the default values in the 
first window. Enter a drain elevation of 220 feet and press F2 to apply this value to the remaining 
rows. 
 Type: 220 under Drain Elevation (ft) 
 (or F2) to assign this value to the entire 
 column 
 [Use Default Conductance] to specify conductance, rather than calculate based on 
 other inputs 
 Type: 1500 in the Conductance field 
 (or F2) to assign this value to the entire 
 column 
 Finish 
Now re-translate and run the model, and review the results: 
 Single Run click this workflow step directly from the workflow 
 navigator 
Make sure that MODFLOW-2005, MODPATH and ZoneBudget are all selected in the single 
engines workflow step. 
  ZONEBUDGET ensure that Zone Budget is selected and active 
  MODPATH ensure that MODPATH is selected and active 
 (Next Step) from the workflow navigator panel 
 to translate input files 
 (Next Step) from the workflow navigator panel 
 to run the model engines 
The MODFLOW-2005 model should run in a few moments, quickly followed by the ZoneBudget 
and MODPATH engines. The entire model run should take no more than 1 minute to run. 
Visual MODFLOW Exercise: Drumco – Part 2 
 
© Waterloo Hydrogeologic Page 62 
 (Next Step) from the workflow navigator panel 
 View Maps 
 
As you can see, by decreasing the excavation depth (i.e. increasing the Drain bottom elevation 
by 6 feet), the drain allows contaminant particles to reach the industrial water supply well. Thus, 
the interceptor trench remedial approach as re-designed here is ineffective in capturing the 
contaminant particles. If you have time after the end of the laboratory exercises, feel free to 
come back to this portion of the exercise and re-design the drain system once more using a 
different design scenario. 
Now is a good time to save the project: 
 File / Save or from the main toolbar 
If you would like to continue this exercise, please follow the instructions provided below. In Part 6 
of this exercise, you will evaluate the effectiveness of a funnel-and-gate system to capture and 
treat the groundwater contamination plume. 
Visual MODFLOW Exercise:Drumco – Part 2 
 
© Waterloo Hydrogeologic Page 63 
PART 6: REMEDIAL FEASIBILITY AND DESIGN – FUNNEL AND GATE SYSTEM 
OR PERMEABLE TREATMENT WALLS 
The fourth and final remedial option to be evaluated is a variation of the treatment wall 
technology for the in situ clean-up of contaminated groundwater. Using the natural groundwater 
flow gradient, contaminated groundwater moves through a specially prepared treatment zone 
designed to reduce the dissolved contaminant concentration through a variety of processes. 
These processes can be both biological and chemical, and include reductive dechlorination, 
precipitation, sorption, oxidation/reduction, fixation, or degradation. The use of zero-valent iron 
filings for the removal of chlorinated hydrocarbons, such as TCE, is one well-known example of 
the application of treatment wall technology. 
The funnel-and-gate system you will be designing relies on permeable treatment wall technology, 
but includes low permeability walls to re-direct the migrating contaminant plume through the 
treatment zone (see Starr and Cherry reference below). 
 
 
Design Issues 
Major design issues associated with a funnel-and-gate permeable treatment wall system include 
the selection of reactive media, residence time of the contaminated water in the treatment zone, 
and calculation of the reactive material’s life span. 
However, the design professional must also consider potential negative effects on the 
groundwater system from the construction of the low-permeability walls. Changes to the flow 
gradient and direction have been observed in actual funnel-and-gate systems, resulting in 
unanticipated spreading of the contaminated groundwater in both the horizontal and vertical 
directions. 
Visual MODFLOW Exercise: Drumco – Part 2 
 
© Waterloo Hydrogeologic Page 64 
Fortunately, the potential negative effects of these systems can be studied in detail using your 
three-dimensional Visual MODFLOW model prior to the actual construction of the remediation 
system. In this exercise, you will test the operational effectiveness of a funnel-and-gate system 
and collect design data to help achieve optimal efficiency (i.e. flow rate through the treatment 
cell and indirectly the residence time within the treatment cell). 
Assigning the Horizontal Flow Barriers / Walls 
The impermeable walls of the funnel-and-gate system will be simulated using the Horizontal Flow 
Barrier (HFB) package of MODFLOW 2005. Once again, we will need to create some new data 
objects to represent the walls. But first, let’s clone our initial model run once again for this new 
scenario. 
 Right-click ‘Run’ right-click the original model run under the Model 
 Explorer 
 Clone Model Run… click this button from the menu that appears 
A new model run (Run4) will appear under the Model Explorer. Ensure that you are viewing the 
numerical workflow for this new model run. 
 Right-click ‘Run4’ under the Model Explorer 
 Open Related Workflow(s)… click this button from the menu that appears 
Now we will create the new wall data objects, and then we will use the drawing tools to populate 
the new objects with actual data. 
 Right-click in the Data Tree 
 Create New Data Object… from the menu that appears 
A new window called ‘Create New Data Object’ will open. 
 Data Type = Polyline 
 Data Name: Wall5 type this value for Data Name 
Repeat the steps above and create the new object Wall6. Wall5 and Wall6 will be used to 
create an impermeable barrier to funnel water toward the permeable treatment zone. 
Now we will use the Visual MODFLOW Flex drawing tools to populate the new data object with 
data (i.e. coordinates) 
 Window > New 2D Window from the main menu 
 Background color: white 
  DRUMCO from the Data Tree 
  Recharge 1 from the Model Explorer, under Run2 
Visual MODFLOW Exercise: Drumco – Part 2 
 
© Waterloo Hydrogeologic Page 65 
 [Zoom to Box] zoom around the area of the Drum Disposal Area 
Now activate Wall5 and draw a line using the following steps and the coordinates listed on the 
following page: 
  Wall5 activate this object in the Data Tree 
Note: the currently selected data object is shown at the 
bottom left of the 2D viewer, next to the ‘Layer’ field. Only 
the currently selected data object can be edited. 
 [Pick Mode] enable pick mode by clicking the button in the toolbar 
 [Begin edit] to begin ‘Edit’ mode 
 [Add polyline] to add a polygon to this data object 
 Draw the polyline: left-click to start and double-click to end 
o The line will extend from the first coordinate below to the 2nd 
▪ X1,Y1 = 1858, 2740 
▪ X2,Y2 = 1858, 1800 
 [End Edit] to end edit and accept changes to data object 
You will now repeat these steps for Wall6 using the approximate start/end coordinates listed 
below: 
Wall6: X1,Y1 = 975, 1753; X2,Y2 = 1858, 1753 
Now return to the Run4 workflow and create new wall boundary conditions using the new data 
objects. 
 Right-click ‘Run4’ under the Model Explorer 
 Open Related Workflow(s)… click this button from the menu that appears 
 Define Boundary Conditions click this workflow step directly from the workflow 
 navigator 
 Layer: 1 ensure you are viewing model layer 1 
 Wall(HFB) select this boundary condition type from the list 
 shown under the Toolbox 
 Assign 
The Define Wall Boundary Condition window will open. Enter the following info: 
 Name: Wall5 type Wall5 in the name field 
 Wall5 select this object from the Data Tree 
 [Select Polyline] to use this object 
Visual MODFLOW Exercise: Drumco – Part 2 
 
© Waterloo Hydrogeologic Page 66 
 ground select this data object from the Data Tree 
 [Top Horizon] to use this object 
 Surface2 select this data object from the Data Tree 
 [Bottom Horizon] to use this object 
 Type: 1e-7 for Conductivity (cm/s) 
 Type: 3 for Thickness (ft) 
Repeat these steps using Wall6 and the same surfaces, conductivity and thickness values as 
above. 
 Wall(HFB) select this boundary condition type from the list 
 shown under the Toolbox 
 Assign 
The Define Wall Boundary Condition window will open. Enter the following info: 
 Name: Wall6 type Wall5 in the name field 
 Wall6 select this object from the Data Tree 
 [Select Polyline] to use this object 
 ground select this data object from the Data Tree 
 [Top Horizon] to use this object 
 Surface2 select this data object from the Data Tree 
 [Bottom Horizon] to use this object 
 Type: 1e-7 for Conductivity (cm/s) 
 Type: 3 for Thickness (ft) 
When you’re finished assigning these new wall boundary conditions they should look something 
like the image below (for layers 1 and 2). The gap between the two wall sections is purposely 
present to simulate the flow effects of a gate or treatment cell, through which groundwater flow 
is channelled. These gates will often contain a synthetic or enhanced porous media which consists 
of a mixture of bionutrients or oxygen that enhances the biodegradation of the dissolved 
contaminants, or an iron-filings-and-sand mixture to treat the water using abiotic reductive 
dechlorination. 
Note that the two walls we installed here can consist of myriad low-permeability materials, 
including steel sheet pilings. Because interlocking sections of steel sheet pilings are thin and thus 
relatively economical to install, it is often less expensive to design the system so that it uses sheet 
pilings wherever possible — as opposed to constructing three-feet-thick walls from somewhat-
less-permeable materials such as clay. 
 
Visual MODFLOW Exercise: Drumco – Part 2 
 
© Waterloo Hydrogeologic Page 67 
 
Assigning the Zone Budget Areas 
In order to design the gate (contaminant reduction cell) and predict the residence time of the 
contaminated water, it is necessary to determine the flow rate passing through the gate. To 
determine water balances in specific zones throughout themodel, you will utilize the Zone 
Budget option that allows you to define any “zone” or area within the model domain for which a 
detailed water balance is to be calculated. This is different than the basic mass balance listing we 
saw earlier that only summarizes the total flows for all wells and each boundary condition type 
(drains, rivers, etc.). 
We’ll assign a Zone Budget zone to the cell in between our two impermeable walls, since this cell 
corresponds to the treatment zone in our hypothetical reactive barrier. 
 Define Zone Budget Zones click this workflow step from the workflow navigator 
  Walls turn on Walls 5 and 6 to help you find the required cell 
  Layer: 1 ensure that you are viewing model Layer 1 
 Zoom to the Drum Disposal Area 
 Assign > Single click the button under the Toolbox 
Visual MODFLOW Exercise: Drumco – Part 2 
 
© Waterloo Hydrogeologic Page 68 
 Click once on Row 45, Column 29 (the cell between Wall5 and Wall6) 
 Finish 
A Create New Zone Budget Zone window will open. 
 New click this button to assign the cells to a new zone 
  Layer 1 assign the new Zone Budget zone to layer 1 
  Layer 2 also assign the new Zone Budget zone to layer 2 
 OK to accept the remaining settings and create new zone 
After creating the new Zone Budget zone the selected cell will turn blue, as shown in the image 
below: 
 
Visual MODFLOW Exercise: Drumco – Part 2 
 
© Waterloo Hydrogeologic Page 69 
Assigning Reduced Recharge 
We will assume the hydraulic conductivity of the permeable wall (Zone #2) is the same as the 
aquifer surrounding it. If not, one would assign a different hydraulic conductivity to the cell(s) 
representing the treatment zone. 
We will simulate a low-permeability cover by assigning a lower recharge rate within the walled 
area. First, make sure that you are viewing layer 1. 
 Define Boundary Conditions click this workflow step directly from the workflow 
 navigator 
  Layer: 1 ensure that you are viewing model Layer 1 
 Recharge select this boundary condition type from the list 
 shown under the Toolbox 
 Assign > Polygon button under the Toolbox 
 Select a rectangular area delineated by Wall5 and Wall6 
 Finish button under the Toolbox 
 Next >> in the Define Boundary Condition window 
 Schedule: Static set this boundary condition to a static schedule 
 (change from transient) 
 Type: 2 under the Recharge (in/yr) field 
 (or F2) to assign this value to the entire 
 column 
 Type: 0 under the Ponding (ft) field 
 (or F2) to assign this value to the entire 
 column 
 Finish to accept values and create the new recharge 
 boundary condition 
If you zoom out and review all recharge zones in Layer 1 your display should look like the image 
below (notice the new recharge zone in the drum disposal area): 
Visual MODFLOW Exercise: Drumco – Part 2 
 
© Waterloo Hydrogeologic Page 70 
 
Running the Model and Viewing the Results 
You will now translate and run the updated model. 
 Single Run click this workflow step directly from the workflow 
 navigator 
Make sure that MODFLOW-2005, MODPATH and ZoneBudget are all selected in the single 
engines workflow step. 
  ZONEBUDGET ensure that Zone Budget is selected and active 
  MODPATH ensure that MODPATH is selected and active 
 (Next Step) from the workflow navigator panel 
Visual MODFLOW Exercise: Drumco – Part 2 
 
© Waterloo Hydrogeologic Page 71 
 to translate input files 
 (Next Step) from the workflow navigator panel 
 to run the model engines 
The MODFLOW-2005 model should run in a few moments, quickly followed by the ZoneBudget 
and MODPATH engines. The entire model run should take no more than 1 minute to run. 
 (Next Step) from the workflow navigator panel 
 View Maps 
Turn on the following objects/results: 
• Forward Particles 
• Heads 
• Wells (Well 1) 
• Walls (Wall5, Wall6) 
• DRUMCO (site map) 
Ensure you are viewing model layer 1 and then zoom in a bit. Your display should look similar to 
the image below: 
Visual MODFLOW Exercise: Drumco – Part 2 
 
© Waterloo Hydrogeologic Page 72 
 
You’ll notice that the steep gradients are directing some of the particles to the left of the barrier 
wall. The equipotential contours show a steep hydraulic gradient at the wall, the result of a 
groundwater mound that has formed on the upgradient side of the wall. You can also illustrate 
this mounding in cross-sectional view. 
You may turn off the Layer view and instead review results through Column 24. Apply a vertical 
exaggeration of 30, and you should see an image similar to the following: 
Visual MODFLOW Exercise: Drumco – Part 2 
 
© Waterloo Hydrogeologic Page 73 
 
This display illustrates groundwater flow being driven through the funnel-and-gate system 
creating mounding at the upgradient side of the “gate”. However, you should also note that the 
vertical downward gradient is also much steeper and could promote downward migration of the 
groundwater plume. This example demonstrates the importance of conducting a particle-
tracking study to determine the preferred migration pathways of the contaminant particles. 
From the figures above, it is clear the funnel-and-gate remediation system does not effectively 
channel the groundwater plume. Most of the particles are either migrating around the edge of 
the wall, or are moving downward through the lower conductivity zone and under the funnel 
wall. 
How long does it take a contaminant particle to travel through the underlying confining layers? 
Count the time markers on the particle pathlines to find out, as each marker represents 365 days. 
In plan view, the particles appear to be travelling through the funnel walls. The downward 
migration of the contaminant particles through the lower conductivity zone is the result of 
groundwater mounding on the upgradient side of the funnel wall, which created a significant 
Visual MODFLOW Exercise: Drumco – Part 2 
 
© Waterloo Hydrogeologic Page 74 
vertical downward flow gradient. Therefore, the system as it is currently designed, does not 
properly 'funnel' the groundwater through the 'gate'. 
The solution is to assign a high conductivity zone (representing a french drain) on the upgradient 
size of the funnel. This drain will reduce the heads on the upgradient side of the funnel and 
promote flow toward the gate. This is something that you can experiment with yourself. 
The next step is to determine the flow rate of the groundwater through the gate (Zone #2). 
 View Charts click this workflow step directly from the workflow 
 navigator 
 Zone Budget click the button at the top-left corner of the View 
 Charts interface 
You will then be transferred to the Zone Budget output display screen. This screen contains four 
distinct plots to summarize the flow data for the user defined flow zones. Select the Time Step 
graph for a breakdown of flows in/out of the Zone Budget zones, broken down into the various 
boundary conditions associated with that zone. 
The first results displayed will be for Zone 1 by default. And Zone 1 represents the entire model 
domain by default. To view the results for Zone 2 (i.e. the gate) you can select Zone 2 from the 
table at the top left. The reference Zone # and Time Step are indicated at the top section of the 
window. The Time Step graph for Zone 2 should look like the image below (you can click any bar 
to display exact values): 
Visual MODFLOW Exercise: Drumco – Part 2 
 
© Waterloo Hydrogeologic Page 75 
 
As you can see from the Zone Budget graphs, total flow in/out of Zone 2 is approximately 1,220 
ft3/day. The vast majority of flow into Zone 2 (the gate) comes from Zone 1 (i.e. bulk GW flow). 
Only a small portion of flow into Zone 2 is contributed from recharge. Using these flow rates, the 
mass loading rate can be determined and an expected life span of the treatment materialscan 
be estimated. 
Take some time to display the results of the funnel and gate design in the 3D viewer. Turn on the 
wall boundaries, forward pathlines and heads (displayed as a color map with isolines in Layer 1). 
You may also turn on the regional pumping wells. Finally, activate structural zone 2. Your display 
should look something like the image below, which clearly shows particle pathlines going under 
and around the barrier wall: 
Visual MODFLOW Exercise: Drumco – Part 2 
 
© Waterloo Hydrogeologic Page 76 
 
Based on these results, the funnel-and-gate remedial approach may not be a feasible alternative 
for remediation, given the geologic and hydrogeologic conditions at the site. 
However, you could continue your feasibility study by modifying the funnel-and-gate system in 
the following ways: 
1. Use a wider gate to trap the escaping contaminant particles. 
2. Add additional gates to the model domain in an attempt to collect the escaping particles. 
3. Add a north-south component to the funnel wall at the western edge to capture the 
horizontal fugitive flow. 
With any approach, you will have to contend with the formation of a vertical gradient that is 
driving the downward migration of contaminant particles. If you have time during this exercise, 
try modifying the funnel-and-gate design to provide a complete funnel of the groundwater plume 
through the treatment cell. 
This completes the Drumco site simulation and clean-up exercise. 
© Waterloo Hydrogeologic 
 
Visual MODFLOW Exercise: ChemWest 
Monitored Natural Attenuation as a Remedial Alternative 
 
 
 
ChemWest Laboratories Ltd. 
Westville, U.S.A. 
 
 
 
 
 
 
 
© Waterloo Hydrogeologic Page 2 
Visual MODFLOW Exercise: ChemWest 
 
 
 
 
ChemWest Outline 
Part 1: Conceptual Model Development .......................................................................................6 
1.1. Geography ...................................................................................................................................... 6 
1.2. Geology and Stratigraphy ............................................................................................................... 6 
1.3. Hydrology and Hydrogeology ......................................................................................................... 7 
1.4. Define the Steady-State Water Table ............................................................................................. 8 
1.5. Sand and Gravel Hydraulic Conductivity ........................................................................................ 8 
Part 2: Flow Model Construction ..................................................................................................9 
2.1. Starting a New Project .................................................................................................................... 9 
2.2. Import Surfaces ............................................................................................................................ 13 
2.3. Define Model Grid ........................................................................................................................ 14 
2.4. Import Base Map .......................................................................................................................... 18 
2.5. Define Default Flow Properties .................................................................................................... 20 
2.6. Creating a Refined Grid ................................................................................................................ 22 
2.7. Refining Model Layers .................................................................................................................. 25 
2.8. Define Model Extents ................................................................................................................... 28 
2.9. Define Aquifer Properties ............................................................................................................. 30 
2.10. Assigning Boundary Conditions ................................................................................................ 35 
2.11. Assigning Aquifer Recharge ...................................................................................................... 46 
2.12. Define Calibration Targets ........................................................................................................ 48 
2.13. Assign Zone Budget Zones to Deer Creek ................................................................................. 53 
Part 3: Calibration ...................................................................................................................... 56 
3.1. Run and calibrate the model ........................................................................................................ 56 
3.2. Calibration Statistics ..................................................................................................................... 57 
Part 4: Transport Simulation Set-up ............................................................................................ 63 
4.1. Introduction .................................................................................................................................. 63 
4.2. Basic Parameters and Transport Boundaries ............................................................................... 63 
4.3. Inactive-for-Transport Region ...................................................................................................... 67 
4.4. Concentration Observation Wells ................................................................................................ 68 
4.5. Solution Method and Output Times ............................................................................................. 69 
4.6. Transport Scenarios ...................................................................................................................... 71 
4.6.1. Run2 – Transport with adsorption only; no bioremediation or pump-and-treat ................. 71 
4.6.2. Run3 – Same as Run2 plus a 50-GPM pump-and-treat system ............................................ 72 
4.6.3. Run4 – Same as Run2 plus first-order decay (natural attenuation) ...................................... 72 
4.7. Comparison of Remedial Options ................................................................................................. 72 
4.7.1. Remedial Objectives .............................................................................................................. 73 
4.7.2. Visualizing Results as Breakthrough Curves .......................................................................... 73 
4.7.3. Visualizing Model Results in 3D ............................................................................................ 74 
 
Figures 
Figure 1. ChemWest Site Map 
Figure 2. Three-dimensional Image of the Model Domain 
Figure 3. Cross-section Distribution Map 
Figure 4. Ground Surface Elevation (feet) 
© Waterloo Hydrogeologic Page 3 
Visual MODFLOW Exercise: ChemWest 
 
 
 
 
Figure 5. Sand/Gravel Surface Elevation (feet) 
Figure 6: Shale Bedrock Surface Elevation (feet) 
Figure 7. Cross-section A-A’ 
Figure 8. Cross-section B-B’ 
Figure 9. Observed Head Measurements 
Figure 10. Hydraulic Conductivity of Sand and Gravel 
 
Appendices 
 Appendix A – Interpreted cross-sections C to G 
 Appendix B – Stratigraphic summary table (strat.xls) 
 Appendix C – Figures for comparison during model construction and calibration 
 Appendix D – Sample borehole logs for cross-sections 
 Appendix E – Calibration data (calpts.txt) 
 
© Waterloo Hydrogeologic Page 4 
Visual MODFLOW Exercise: ChemWest 
 
 
 
 
Exercise Summary 
This exercise is designed to build your skills in groundwater model design, construction and 
calibration using data from an actual modeling project that Waterloo Hydrogeologic,Inc. was 
retained to complete. You will receive a thorough introduction to the process of building a 
groundwater flow and contaminant transport model using Visual MODFLOW. After you have 
built and successfully calibrated your flow model, you will evaluate the following two remedial 
alternatives: 
• pump and treat, and 
• monitored natural attenuation. 
After completing this exercise, you will have increased your understanding of the following key 
steps in the building of a groundwater model: 
1 Analysis of field data to develop a conceptual site model (representation with essential or 
controlling features only) of the site; 
2 Identification of major surface and subsurface features that control the groundwater 
system; 
3 Creation of variable surface files using mapping tools in Surfer for Windows from field data; 
4 Building a groundwater flow model in Visual MODFLOW Flex; 
5 Import of variable surface files that you created using Surfer and Excel; 
6 Specification of boundary conditions, recharge quantity, and hydraulic conductivity zones; 
7 Model calibration process, including calibration to observed heads and base flow from a 
stream; 
8 How a calibrated groundwater flow model can be applied to simulate actual groundwater 
flow and contaminant transport scenarios, and how to reduce the time required for 
transport simulations by using the inactive transport zone feature in Visual MODFLOW. 
Although the geographic location and the names used in this lab are fictitious, 
this lab is based on a real project, where Waterloo Hydrogeologic/Schlumberger 
Water Services (SWS) was asked to study the potential for natural attenuation as 
a remedial alternative. The model that you will develop is similar to the actual 
model that SWS developed for its client – it differs only in the level of detail, 
which had to be reduced to fit into the time constraints of this course. 
Reference: U.S. EPA, 1999: Use of Monitored Natural Attenuation at Superfund, RCRA 
Corrective Action, and Underground Storage Tank Sites. OSWER Directive 9200.4-17P. 
Washington, D.C. http://www.epa.gov/swerust1/directiv/d9200417.htm, 32 pp. 
© Waterloo Hydrogeologic Page 5 
Visual MODFLOW Exercise: ChemWest 
 
 
 
 
Project Background 
ChemWest Laboratories Ltd. is located on the Norman River in the American Midwest (see 
Figure 1 for a site plan). It has manufactured inorganic and organic industrial chemicals since 
the early 1960s. Benzene was first documented in the groundwater 25 years ago, when it was 
detected in a nearby municipal drinking water well. The municipal well was removed from 
service shortly after the discovery of the contamination. Subsequent investigation revealed a 
dissolved benzene plume originating from an underground storage tank (UST) several hundred 
feet upgradient of the well. A pump and treat recovery program was initiated to hydraulically 
contain the benzene plume and to ultimately capture it. The UST was later excavated along 
with 15,000 tons of contaminated soil. 
After more than ten years of continuous groundwater pumping (more than 500 million gallons 
of groundwater have been extracted), the extent of the benzene plume has diminished 
substantially. Recent groundwater sampling revealed that only four monitoring wells in one 
area of the site contained benzene concentrations above the prescribed groundwater criteria. A 
geochemical study was undertaken, which concluded that the reduced benzene concentrations 
were a result of both naturally occurring biodegradation and extraction through the pump and 
treat system. 
Based on these findings, ChemWest proposed to the U.S. EPA that the pump and treat 
operations be terminated and allow natural biodegradation to eliminate the remaining 
benzene. ChemWest would implement an expanded monitoring program, but would still realise 
a net annual saving of more than $150,000. Waterloo Hydrogeologic was asked to develop a 
numerical groundwater model to assess the feasibility of this plan. 
Terms and Notations 
For the purposes of this tutorial, the following terms and notations will be used. (This assumes 
you are using a right-handed mouse.) 
type - type in the given word or value 
↔ - press the <Tab> key 
 - press the <Enter> key 
 - click the left mouse button where indicated 
 - double-click the left mouse button where indicated 
© Waterloo Hydrogeologic Page 6 
Visual MODFLOW Exercise: ChemWest 
 
 
 
 
PART 1: CONCEPTUAL MODEL DEVELOPMENT 
A conceptual model is a simplification of the actual geologic and hydrogeologic conditions that 
captures the essential aspects of the hydrogeologic system in terms of the questions being 
asked. The development of the conceptual model is a very important first step in building a 
valid groundwater model because it must identify the features that control the hydrogeology of 
the site. 
In the subsections below, you will be provided with information about features at the site that 
you will use to develop a valid conceptual model. The tasks below represent the major steps 
required in the building of a model. 
1.1. Geography 
The site is situated in a broad, fluvial valley beside the Norman River, which exerts an influence 
on the local groundwater flow (see Figure 1). Along the eastern boundary of the site, the shale 
bedrock outcrops and rises sharply to 200 feet above the valley floor. The Norman River is up to 
1500 feet wide in places and flows north to south through the valley. Near the site there is a 
flood-control dam creating a 10-foot difference in the river water levels upstream and 
downstream of the dam. Four hundred feet downstream of the dam is Deer Creek, which flows 
generally east to west across the site. On the site itself there are two small ponds. Figure 2 is a 
perspective view of the site looking approximately from South/South-West to North/North-
East. 
1.2. Geology and Stratigraphy 
Nearly 100 boreholes and piezometers exist on the site, of which several sample borehole logs 
can be found in Appendix D. Analysis of these borehole data indicates, the primary subsurface 
stratigraphy at the site consists of the following: 
▪ a surficial silty sand, 
▪ an extensive sand and gravel aquifer, and 
▪ the shale bedrock. 
The surficial silty sand exists across the site and ranges in thickness from 5 to 25 feet. It is 
largely unsaturated, with the water table often found in the underlying sand and gravel aquifer. 
The sand and gravel aquifer is also present across the site with a thickness varying from 10 to 
60 feet. The aquifer is present under Norman River, however it pinches out where it intersects 
the valley walls to the east. The sand and gravel aquifer is a major water-bearing unit and has 
historically provided substantial water to local water supply wells. 
The shale bedrock underlies the entire site. East of Norman River, the valley walls consist of 
shale interbedded with minor carbonaceous siltstones and massive fresh-water limestones. The 
© Waterloo Hydrogeologic Page 7 
Visual MODFLOW Exercise: ChemWest 
 
 
 
 
hydraulic conductivity of the valley walls is five orders of magnitude lower than the sand and 
gravel aquifer and can be considered essentially impermeable. 
Surface files representing each of the major stratigraphic layers are included in the ‘Supporting 
Files’ folder for this exercise. The file names and corresponding stratigraphic layers are listed 
below. You may also review the elevation distribution for each of these surfaces by reviewing 
Figures 4-6. 
• Grndsrf.GRD; ground surface horizon (Figure 4) 
• ChemWest_SG.GRD; sand/gravel horizon (Figure 5) 
• Chemwest_Bed.GRD; bedrock surface horizon (Figure 6) 
If you would like to review data sources, the stratigraphic data used to generate these surface 
files can be found in the Excel spreadsheet file STRAT.xls (in the directory C:\vmod\ChemWest). 
This file contains a list of the wells used in the characterization of the site and the elevationsof 
all the stratigraphic contacts. 
Please note that the surface files listed above will be used to define the elevation of our 
numerical model layers, which will have an important bearing on the overall results of our 
model. Using the supporting data files, you could import contact data for each stratigraphic unit 
and interpolate the surfaces directly in Visual MODFLOW Flex. With many available 
interpolation methods and settings, it would be possible to generate many small variations on 
the same surface. Surface files are provided for this exercise, to save time; but please note that 
the generation of model input files is an important part of the modelling process which isn’t 
covered here. 
1.3. Hydrology and Hydrogeology 
An important part of the conceptual model is the conceptualization of the site hydrology and 
hydrogeology. The site hydrology includes fluxes to the groundwater such as: 
• groundwater recharge from precipitation (depends on the surface characteristics), 
• overland flow that infiltrates to the groundwater along a boundary, 
• direct recharge from surface water bodies, 
• direct groundwater flow to the model area along a boundary, and 
• artificial groundwater recharge and injection. 
It also includes groundwater fluxes out of the system, such as: 
• evaporative losses, 
• transpiration, 
• discharge as springs, 
• baseflow to streams and rivers, and 
• pumping from wells. 
© Waterloo Hydrogeologic Page 8 
Visual MODFLOW Exercise: ChemWest 
 
 
 
 
In the case of the Chemwest site, the key features to understanding the flow system are: 
• the Norman River, 
• the bedrock valley, 
• the lakes on site, 
• the groundwater flow gradient around the dam, and 
• Deer Creek. 
These hydraulic features should be carefully considered when you develop your expected 
groundwater table contour map in the next task. 
In addition to the surface water bodies, you must also consider the annual rainfall, which is 
about 40 inches/year, and the ground surface, which is generally grass-covered between the 
buildings and roads. 
1.4. Define the Steady-State Water Table 
Based on the water level data presented in Figure 9, use a pencil to contour your concept of 
how the water table should have appeared, prior to initiation of remedial pumping. Later you 
will compare your contour map with your model results to assess whether your conceptual 
groundwater flow model corresponds to your Visual MODFLOW Flex model. 
1.5. Sand and Gravel Hydraulic Conductivity 
Slug tests conducted in the sand/gravel aquifer demonstrated a range of hydraulic 
conductivities from 3.16 ft/day to 235 ft/day. Figure 10 gives the distribution of hydraulic 
conductivity for the slug tests performed across the site. The slug tests were interpreted using 
the Bouwer-Rice method in the program AquiferTest Pro. 
© Waterloo Hydrogeologic Page 9 
Visual MODFLOW Exercise: ChemWest 
 
 
 
 
PART 2: FLOW MODEL CONSTRUCTION 
The following tasks describe the general steps needed to construct your groundwater flow 
model based on the conceptual model developed in Part 1. 
2.1. Starting a New Project 
On your Windows desktop, you will see an icon for Visual MODFLOW Flex 
 Visual MODFLOW Flex to start the program. 
The following Visual MODFLOW Flex window will appear: 
 
To create a new project: 
 File / New Project from the top menu bar 
© Waterloo Hydrogeologic Page 10 
Visual MODFLOW Exercise: ChemWest 
 
 
 
 
A Create Project dialog box will be displayed prompting you to enter the project name of the 
new Visual MODFLOW Flex project. Enter the following data, and ensure the units are set 
according to the table below. When you’re finished the Create Project window should look like 
the image below: 
 Type: ChemWest as the project name 
 Browse button under Data Repository 
 Select a directory on the hard drive (or use the default location) 
Note: By default, new Visual MODFLOW Flex projects 
will be saved to the following location - 
[C:\Users\<username>\Documents\Visual MODFLOW 
Flex\Projects] 
 Concentration = ug/L 
 Conductivity = ft/d 
 Length = ft 
 Mass = kg 
 Pumping Rate = GPM 
 Recharge = in/yr 
 Time = day 
 
 OK button in the lower right corner of this window 
The following window will then appear: 
© Waterloo Hydrogeologic Page 11 
Visual MODFLOW Exercise: ChemWest 
 
 
 
 
 
The Select Modeling Scenario window allows you to choose whether to proceed with the 
Conceptual or Numerical modeling workflow. The conceptual modeling workflow allows you to 
import all data objects into Visual MODFLOW Flex and to build a conceptual site model (CSM). 
The CSM can then be used as a starting point for several different numerical models. In other 
words, numerical model (i.e. with different grid types, engines, etc.) can be quickly and easily 
created based on the same conceptual modeling. This makes it easy for the user to manage 
several different numerical models with slight variations. 
Conceptual modeling is not covered in this exercise, so we will proceed with the numerical 
modeling workflow: 
 Numerical Modeling 
Proceeding with the numerical modeling workflow will bring you to the first step in the that 
workflow, which is the Define Modeling Objectives step. This step allows you to specify 
whether you will be running a fully saturated or variably saturated model, whether 
contaminant transport will be included, which flow/transport engines will be utilized, etc. You 
will see the following window open: 
 
© Waterloo Hydrogeologic Page 12 
Visual MODFLOW Exercise: ChemWest 
 
 
 
 
 
At this stage we will specify the following ‘model objectives’: 
 Start Date: 1/1/2017 type or use calendar menu to enter January 1, 2017 
  Transport Active to activate the transport engines 
We will keep the remaining default flow parameter values. 
 Next Step proceed to the next step in the workflow 
The Define Numerical Model workflow step will appear. At this stage we decide whether we 
would like to import an existing finite difference grid, or to create a new one. 
 Create Grid button from the main window 
© Waterloo Hydrogeologic Page 13 
Visual MODFLOW Exercise: ChemWest 
 
 
 
 
This will bring you to the Create Grid step in the numerical modeling workflow. At this step you 
will specify the boundary/extents of your model and the structure of your model’s grid. Your 
screen should look like the image below: 
 
2.2. Import Surfaces 
We would like to use the stratigraphic surfaces discussed in Part 1.2 to help us define the 
vertical discretization of our model layers. Therefore, we’ll take a few moments to import 
model elements before proceeding any further with the numerical modeling workflow. 
Importing data objects into Visual MODFLOW Flex is a simple process. In order to import the 
surfaces, follow the instructions below: 
 File/Import Data… from the main menu, the Data Import 
 window will open 
 Surface from the Data Type drop-down menu 
 […] button next to Source File field, to select file 
 
© Waterloo Hydrogeologic Page 14 
Visual MODFLOW Exercise: ChemWest 
 
 
 
 
A dialogue box opens that allows you to browse for the appropriate file. Browse to the 
supporting files folder and choose the following file: 
 Grndsrf.GRD surface object representing the ground surface 
 Open 
 Type: GroundSurface in the Name field, to rename the object 
 Next >> to accept name/file and proceed to the next step 
 Next >> to accept coordinate system and proceed to the 
 next step 
 Next >> to accept default data mapping 
 Finish to complete the surface import 
Repeat the same process to import the other surfaces, Chemwest_SG (rename data object to 
SandGravel) and Chemwest_Bed (Rename data object to Bedrock). When you are done, the 
Data Explorer window should look like the image below: 
 
2.3. Define Model Grid 
Now you will proceedto define the model grid. You should still be viewing the Create Grid 
workflow step. If you’re not on the Create Grid step you can return directly to this step by 
simply clicking the step directly in the workflow navigator. 
To define the finite difference grid you will specify the number of rows, columns, and layers to 
be used in the model, and the overall extent/size of the numerical model. Under the Grid Size 
frame enter the number of model rows and columns: 
© Waterloo Hydrogeologic Page 15 
Visual MODFLOW Exercise: ChemWest 
 
 
 
 
 Rows = 71 enter under the Grid Size frame 
 Columns = 46 enter under the Grid Size frame 
Under the Grid Extents frame, specify the spatial extents of the grid: 
 Xmin = 1000 enter under the Grid Extents frame 
 Xmax = 7000 enter under the Grid Extents frame 
 Cell Width automatically calculated 
 Ymin = -1500 enter under the Grid Extents frame 
 Ymax = 7000 enter under the Grid Extents frame 
 Cell Height automatically calculated 
For this exercise, you will ignore the option “Calculate extents from a polygon object” 
Next, specify the parameters for the vertical grid discretization: 
 2 for the Number of Layers 
  Enter on the keyboard 
Now we need to use the imported surfaces in order to define the elevation for each layer: Layer 
1 – Top, Layer 2 – Top and Layer 2 – Bottom with GroundSurface, SandGravel and Bedrock, 
respectively. 
 GroundSurface select object in the Data Explorer window 
 corresponding to Layer 1 - Top 
 SandGravel in the Data Explorer window 
 corresponding to Layer 2 – Top 
 Bedrock in the Data Explorer window 
 corresponding to Layer 2 – Bottom 
The Create Grid workflow window should now look like the image below (viewer window has 
been resized to display the general shape of the model area): 
© Waterloo Hydrogeologic Page 16 
Visual MODFLOW Exercise: ChemWest 
 
 
 
 
 
 Create Grid button near the top of the window. 
Visual MODFLOW Flex will then construct 46 columns  71 rows  2 layers finite difference grid 
with uniform grid spacing in both the X and Y directions, and will automatically create the 
model run Input tree structure, as shown below. 
© Waterloo Hydrogeologic Page 17 
Visual MODFLOW Exercise: ChemWest 
 
 
 
 
 
Proceed to the next step and you will be taken to the View Grid workflow step as shown in the 
following figure. 
 Next Step proceed to the next step in the workflow 
 
© Waterloo Hydrogeologic Page 18 
Visual MODFLOW Exercise: ChemWest 
 
 
 
 
The View/Edit Grid workflow step is available in case you need to make any changes to your 
grid. For now, we will simply use the grid as originally created, which means we can skip this 
step. 
The next step will be to define the model properties, including hydraulic conductivity, storage 
and porosity properties. It will be helpful if we can use a site map to help us assign properties, 
so before proceeding to the next workflow step we will import a site map. 
2.4. Import Base Map 
You will select a shapefile to be used as a background base map for your model. 
 File / Import Data… from the main menu, the Data Import window opens 
 Dxf from the Data Type menu 
 […] button next to Source File field, to select file 
A dialogue box opens that allows you to browse for the appropriate file. Browse to the 
supporting files folder and choose the following file: 
 Chemwest.dxf 
 Open 
 Type: BaseMap in the Name field, to rename the object 
 Next >> to accept name/file and proceed to the next step 
 Next >> to accept default coordinate system 
 Finish 
The new data object will appear as the last item in the data tree. We can view the basemap in a 
new 2D Viewer window. 
 Right-click on Basemap in the Data tree 
 2D Viewer from the pop-up menu that appears 
© Waterloo Hydrogeologic Page 19 
Visual MODFLOW Exercise: ChemWest 
 
 
 
 
 
The basemap will become visible in a new view window which appears as a new tab, as shown 
below. Please note that the background color of the 2D viewer has been switched to white in 
the image below. The background color may be updated by right-clicking and selecting 
‘Background color’. 
Close the viewer window by selecting the ‘X’ in the tab labelled ‘2D Viewer -1’. 
 
© Waterloo Hydrogeologic Page 20 
Visual MODFLOW Exercise: ChemWest 
 
 
 
 
 
 [x] to close ‘2D Viewer – 1’ tab 
2.5. Define Default Flow Properties 
We will now define the groundwater flow properties for our numerical model. Currently the 
entire model domain has a homogeneous property distribution, and every cell is assigned the 
default property values listed in the Define Modeling Objectives step. Model default values can 
be updated in the Project Settings window (File / Project Settings / Model Defaults), and cell-
by-cell values can be updated during the Define Properties workflow step. Later in this exercise 
we will assign cell-by-cell values for our lower layer. But for now we will simply assign the same 
flow properties to the entire model domain. 
 Next Step proceed to the next step in the workflow 
 Conductivity ensure this property group is selected from the first 
 menu under the Toolbox 
 Edit button under the Toolbox 
The Edit Property window will open, displaying the default hydraulic conductivity values (Kx, Ky 
and Kz), as shown below: 
© Waterloo Hydrogeologic Page 21 
Visual MODFLOW Exercise: ChemWest 
 
 
 
 
 
For this simple model, we will assume all grid cells have the same hydraulic conductivity (values 
are defined in m/s). Redefine the Kx, Ky and Kz property values by typing new values into any 
cell in the appropriate column and pressing the ‘Assign to column’ button: 
 Type: 4 for Kx 
 (or F2) to assign this value to the entire column 
 Type: 4 for Ky 
 (or F2) to assign this value to the entire column 
 Type: 0.4 for Kz 
 (or F2) to assign this value to the entire column 
 OK to exit the dialogue window 
Next, we will change the storage parameters of the model. 
 Storage ensure this property group is selected from the first 
 menu under the Toolbox 
 Edit button under the Toolbox 
Change the storage parameters as follows; 
 Type: Sy = 0.25 specific yield 
 (or F2) to assign this value to the entire column 
 Type: Ss = 0.005 specific storage (1/m) 
 (or F2) to assign this value to the entire column 
 Type: Ep = 0.25 effective porosity 
 (or F2) to assign this value to the entire column 
© Waterloo Hydrogeologic Page 22 
Visual MODFLOW Exercise: ChemWest 
 
 
 
 
 Type: Tp = 0.30 total porosity 
 (or F2) to assign this value to the entire column 
 
 
 
 OK to accept the storage values 
Now is a good time to save the project. 
 File / Save Project (from the main menu) 
2.6. Creating a Refined Grid 
Before assigning the concentration source, it is important to create a more refined grid in our 
area of interest, where predictions will be made of plume concentration. This will allow us to 
improve the accuracy of the simulated plume and therefore better predict the fate of the 
groundwater contaminant. The preliminary finite difference grid needs to be refined so that the 
grid is reasonably fine for contaminant transport simulations later in the lab. In the original 
model, the grid was refined extensively. However, to keep the run time reasonable for the 
course we suggest that you simply refine the columns by factor two between the Norman River 
and the Main Highway and the rows between about y = 1000 and y = 5000 feet. 
Fortunately, Visual MODFLOW Flex allows us to create multiple numerical representations for 
the site, and derive the inputs for each numerical model from the conceptual objects that were 
generated while drawing the property zones and boundary conditions in Part 1 of this exercise. 
From the Model Explorer tree, locate the ‘Simulation Domain’ folder.Under this, find the item 
‘Model Domain’. 
 Right-click on NumericGrid1 from the Model Explorer, as shown below 
 Edit Numerical Grid… from the menu that appears 
 
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Visual MODFLOW Exercise: ChemWest 
 
 
 
 
 
The following window will appear (please note that you can also access this window from the 
‘View/Edit Grid’ workflow step, by clicking the ‘Edit Grid’ button): 
 
 Type: RefinedGrid for New Grid Name at the top 
Ensure that the ‘Edit Rows’ option is selected, and enter the following values: 
  Edit rows 
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Visual MODFLOW Exercise: ChemWest 
 
 
 
 
 Type: 18 for From 
 Type: 50 for To 
 Type: 2 for row{s} with 
 Apply grid edit press button to apply this row refinement 
Once finished, the display should appear as below. 
 
The rows between the 2 selected gridlines will automatically double. Now, we must perform 
the same task to the columns in the model. 
  Edit Columns 
 Type: 11 for From 
 Type: 30 for To 
 Type: 2 for columns{s} with 
 Apply grid edit press button to apply this column refinement 
The number of columns between these 2 gridlines should automatically double. When the grid 
refinement is complete you should have a total of 104 rows and 66 columns. Your grid should 
appear similar to the following figure: 
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Visual MODFLOW Exercise: ChemWest 
 
 
 
 
 
 OK to apply the grid edits and close the window 
You will see that the new ‘RefinedGrid’ grid has been created in the Model Explorer and a 
separate workflow tab has been opened. We can view the refinement applied to the grid by 
selecting the RefinedGrid checkbox from the Model Explorer at the left-bottom corner: 
  Refined Grid from the list of views 
2.7. Refining Model Layers 
When the new RefinedGrid numerical workflow opened it should have been on the Define 
Properties step, since this was the step we were on when we began the Edit Grid process. 
Before proceeding we will review our model layers. Change to any cross-sectional view (e.g. 
row 47), and increase the vertical exaggeration to 10. 
 □ Layer from the Flex viewer, to deactivate Layer view 
  Row from the Flex viewer, to activate Row view 
 Row = 47 type under the row view 
 Exaggeration = 10 under Exaggeration in the 2D window 
The resulting surfaces in Visual MODFLOW Flex look like the following: 
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Visual MODFLOW Exercise: ChemWest 
 
 
 
 
 
To introduce some detail for the vertical discretization, divide the bottom layer in half. 
 View/Edit Grid go directly to this step by clicking on the 
 workflow navigator 
 Edit layers under the Grid Refinement toolbox 
The following window should appear: 
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Visual MODFLOW Exercise: ChemWest 
 
 
 
 
 
 Type: RefinedChemWest under New grid name 
 Type: 47 under Viewing Row 
 Type: 10 under Exaggeration 
Under the Refine tab for layer editing: 
 Type: 2 under From, to specify the top of layer 
 Type: 2 under To, to specify the bottom of layer 
 Type: 2 under Factor, for the factor of refinement 
Now your Edit Layers window should appear as seen below: 
 
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Visual MODFLOW Exercise: ChemWest 
 
 
 
 
 Apply edit press button to apply this layer refinement 
 OK 
You should have a total of three layers in your model when you finish this task. An image of row 
47 is shown below. If you do not have three layers in your model at this point please ask your 
instructor for assistance. 
 
2.8. Define Model Extents 
Where the shale bedrock rises to pinch out the sand aquifer and form the valley uplands to the 
east, a no-flow boundary can be assigned. The location of this boundary can be deduced from 
your completed hydrogeologic sections – it is located just east of the highway. Or use the 
highway as an approximate guide. The location of the pinchout is also highlighted in the site 
map, as indicated by a pink line near the highway. We will make the upland area (to the East of 
the highway) inactive. 
Ensure you are still on the View/Edit Grid workflow step, and switch to plan view: 
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Visual MODFLOW Exercise: ChemWest 
 
 
 
 
 View/Edit Grid go directly to this step by clicking on the 
 workflow navigator 
  Layer from the Flex viewer, to activate Layer view 
 □ Row from the Flex viewer, to deactivate Row view 
  BaseMap to activate the Base Map from the Data Explorer 
 Inactive from the drop down menu under Inactive Cells 
 Assign under the Inactive Cells toolbar 
 Polygon from the menu that appears 
 Draw a polygon to cover the uplands area as seen in the image below 
NOTE: for this exercise the inactive area has been 
simplified considerably. Notice how the image on the 
following page makes a simple area inactive (loosely 
following the ‘Approximate Location of Sand & Gravel 
Pinch-Out’ (i.e. the pink line on the site map), instead of 
closely following the actual ‘Uplands’ area. 
 Double click to close the polygon 
 Right Click to open the polygon menu 
 Finish to finish creating polygon 
 
You may need to update the background color in the Flex viewer to make this task 
easier. Right-click anywhere in the viewer and select ‘Background color’ to update. 
The Assign To Layers window will appear to copy this inactive area to all layers: 
  Select All Layers to assign the Uplands inactive area to all layers 
 OK 
To simulate the effect of the concrete flood control dam on the Norman River, assign an area of 
inactive cells in the first model layer only. 
 Assign inactive cells at flood control dam 
o Rows 62 and 63, from Column 1-7 (total of 14 cells) 
o Layer 1 
The inactive cells will become green. When you’re finished assigning inactive cells to the flood 
control dam and the Uplands area your display should look like the image below: 
 
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Visual MODFLOW Exercise: ChemWest 
 
 
 
 
 
To view the ground surface in three dimensions,  3D in the Views menu bar. This will activate 
the 3D Explorer, which will take a few seconds to load. Feel free to explore the model grid from 
a three-dimensional perspective. 
2.9. Define Aquifer Properties 
The next step is to assign the hydraulic properties to each of the layers. 
In step 2.5 we assigned default flow properties across the entire model domain. To facilitate the 
calibration process for this lab we will assume a uniform value of hydraulic conductivity and 
porosity in the silty-sand unit in Layer 1 (i.e. the values that were entered in step 2.5). We will 
also assume that the default conductivity values apply for the entirety of the Norman River, 
through all layers. 
For the sand and gravel unit (Layers 2 and 3) the hydraulic conductivities must be assigned to 
reflect the values obtained from the slug tests which are mapped in Figure 10. In order to do 
this, we will import the measured conductivity values as a ‘points’ data object. The measured 
values will be used to interpolate a surface representing the distribution of conductivity values 
through the sand and gravel layer. 
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Visual MODFLOW Exercise: ChemWest 
 
 
 
 
 File / Import Data… from the main menu 
 Point from the Data Type menu 
 […] button next to Source File field, to select file 
 Chemwest_wells.xls 
 Open 
 Type: ConductivityMeasured in the Name field 
 Next >> 
 Type: 3 in the From row field (to start importing from 
 Row 3) 
 Next >> 
 Next >> 
 Target field X – Map to: F2 map the X field to column F2 
 Target field Y – Map to: F3 map the Y field to column F3 
 Target field Elevation – Map to: F4 map the Elevation field to column F4 
NOTE: By default the target field for points data sources 
will read ‘Elevation’. However, points data is not limitedto 
elevations; in fact, any attribute data can be included. But 
by default the menu will display ‘Elevation’ as the target 
field. 
 Target field Elevation – Unit category: Conductivity ensure that the unit 
 category for our data is set to conductivity 
 Target field Elevation – Unit: ft/d ensure that the units for our conductivity 
 data is set to ft/d 
The Data Mapping window during the Data Import process should look like the image below: 
 
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Visual MODFLOW Exercise: ChemWest 
 
 
 
 
 Next >> 
 Finish 
You should see a new points data object (ConductivityMeasured) appear in the Data Tree. We 
will now interpolate this data to create a surface representing our conductivity distribution. 
 Right-click ConductivityMeasured from the Data Tree 
 Create Surface… from the menu that appears 
 Type: Conductivity for Surface Name 
 Select ConductivityMeasured from the Data Tree 
 to add selected data object to the Data Source table 
 Interpolation Settings click this tab to review settings 
 X Max = 7000 under Interpolation Domain 
 Y Max = 7000 under Interpolation Domain 
 X Min = 1000 under Interpolation Domain 
 Y Min = -1500 under Interpolation Domain 
 OK 
A message will appear indicating that the surface has been created successfully. You can now 
use this data object to define the distribution of conductivity values within model Layers 2 and 
3. Return to the Define Properties workflow step to make this change: 
 Define Properties go directly to this step by clicking on the 
 workflow navigator 
 Conductivity ensure this property group is selected from the first 
 menu under the Toolbox 
 Assign button under the Toolbox 
 Entire Layer/Row/Column from the menu that appears 
The New Property Zone window will appear. We will create a new property zone and use the 
interpolated ‘Conductivity’ surface to define the conductivity values within the new zone. 
 New click button at top left of window to create a new 
 property zone 
 Kx Method: Use Surface select Surface as the method to define Kx 
 Ky Method: Use Surface select Surface as the method to define Ky 
 Kz Method: Use Surface select Surface as the method to define Kz 
 Select Conductivity select the surface object from the Data Tree 
 Kx: Object press arrow to use Conductivity for Kx distribution 
 Ky: Object press arrow to use Conductivity for Ky distribution 
 Kz: Object press arrow to use Conductivity for Kz distribution 
  Assign to layer ensure the Assign to layers option is selected 
 □ Layer 1 ensure Layer 1is deselected 
  Layer 2 ensure Layer 2 is selected 
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Visual MODFLOW Exercise: ChemWest 
 
 
 
 
  Layer 3 ensure Layer 3 is selected 
Please note that Kz will remain at the default value of 0.4 ft/d. The New Property Zone window 
should now look like the image below: 
 
 OK 
Under the toolbox the 2nd menu provides a list of attributes which can be displayed. For 
conductivity you may display the conductivity zones, or values for Kx, Ky and Kz. We will switch 
the view to Kx values, and your distribution of Kx (and Ky) should look like the image below: 
 Conductivity ensure this property group is selected from the first 
 menu under the Toolbox 
 Kx select Kx from the 2nd menu under the Toolbox 
  Layer: 2 ensure you are viewing Layer 2 
At this stage the distribution of hydraulic conductivity values (Kx) in Layer 2 should look like the 
image below (some display settings have been changed): 
 
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Visual MODFLOW Exercise: ChemWest 
 
 
 
 
2.10. Assigning Boundary Conditions 
There are four important hydraulic boundaries within the active area of the model; Norman 
River, Deer Creek, Salmon Pond and Bass Lake. Although the boundaries could be assigned in 
various ways, we suggest that you use constant head boundaries in Layer 1 ONLY for the 
Norman River, and a River Boundary for Deer Creek, Bass Lake and Salmon Pond. 
Norman River 
Upstream of the dam, the stage elevation of Norman River drops by about 1.0 ft between the 
northern boundary of the model and the dam (602.5 to 601.5 ft AMSL). Downstream of the 
dam, the river stage elevation drops from 587.5 ft at the dam to 586.5 ft AMSL at the southern 
boundary of the model. The start and stop times for these boundary conditions are arbitrary in 
this model because we are assuming steady-state flow. The following table summarizes the 
Norman River elevations. 
 Above Dam Below Dam 
Upstream elevation 602.5 587.5 
Downstream elevation 601.5 586.5 
Visual MODFLOW Flex (v5.0 and earlier) unfortunately do not provide a simple method of 
assigning sloping constant head boundary conditions over a wide area (i.e. greater than 1 cell in 
width). In order to assign a sloping boundary condition on the upstream side of the dam we will 
make use of several minor data management features available in Visual MODFLOW Flex. We 
will follow the following general procedure (more detailed step-by-step instructions are 
included below): 
1) Assign a single polyline from the Northern edge of the model down to the dam 
2) Calculate the head in each intermediate cell using the interpolate function 
3) Export the polyline boundary for processing in Excel 
4) Copy the existing data several times, updating the column # 
5) Save and import the new boundary condition file (which now applies across several 
columns) 
To assign the constant head boundary in the upstream portion of the river, follow these 
instructions: 
 Next Step proceed to the Define Boundary Conditions step in 
 the workflow 
 [Zoom to Box] in order to zoom to a specific area in the model 
 Click and draw an area around the upstream portion of the Norman River 
The layer view should look similar to this (you may need to change the background color and 
activate the site map): 
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Visual MODFLOW Exercise: ChemWest 
 
 
 
 
 
 Constant Heads from the dropdown list under the Toolbox 
 Assign from the Toolbox menu bar 
 Polyline from the menu that appears 
 Draw a line from the top-left most cell (1, 1, 1) in the grid straight down column 1 
to just above the dam (i.e. cell (1, 61, 1)) 
Note: cell IDs above are identified as (layer, row, column) 
 Right-click and select Finish 
The Define Boundary Condition window will open. 
 Next >> to accept default name and proceed 
 Type: 602.5 as the Starting Head (m) and Ending Head (m) for 
 cell (1, 1, 1) 
 Scroll to the bottom 
 Type: 601.5 as the Starting Head (m) and Ending Head (m) for 
 cell (1, 61, 1) 
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Visual MODFLOW Exercise: ChemWest 
 
 
 
 
 While holding CTRL, select both the first and the last rows in the entire table 
 [Interpolate] to interpolate and provide a smooth transition in 
 head values upstream of the Norman River 
After interpolating the starting and ending heads, the Define Boundary Condition window 
should look like the image below: 
 
Before finishing this boundary condition select the ‘Script’ tab within the Define Boundary 
Condition window: 
 Script select this tab in the Define Boundary Conditions 
 window (upper left corner) 
The script tab should look like the image below. On this tab you will find the script for any edits 
you make on the Edit cells tab allowing you to learn the script language. We could continue 
building the boundary condition for the remaining Norman River cells directly in this tab. 
However, simply processing data in Excel may be easier in this case. 
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Visual MODFLOW Exercise: ChemWest 
 
 
 
 
 
 Finish to accept values and create boundary condition 
A new constant head boundary condition should appear in the Model Explorer. We will export 
this boundarycondition and open the file in Excel in order to make some edits. 
 Right-click ‘Constant Head 1’ from the Model Explorer 
 Export… from the menu that appears 
 Browse to a convenient location 
 Save (file name: Constant Head 1) to save the exported boundary condition 
 No when asked whether you’d like to open the file 
 Open the file with Excel 
You will now copy and paste the contents of that file an additional 11 times, each time 
increasing the column number by 1. What you’re doing here is just copying the entirety of the 
boundary condition as it currently exists into subsequent columns. 
NOTE: please ensure that the cell format for the starting 
and ending head columns (i.e. columns G and H) are set to 
number formatting (not scientific) with sufficient decimal 
places (at least 5). Visual MODFLOW Flex requires the data 
to be in simple numerical format for importing. 
When you have finished editing the boundary condition file you can save it and close Excel. You 
will now delete the existing boundary condition and then import the recently edited text file. 
 Right-click ‘Constant Head 1’ from the Model Explorer 
 Delete… from the menu that appears 
 Yes to the warning message that appears 
 Import… button under the Toolbox 
 Browse to the location of the recently edited text file (Constant Head 1.txt) 
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Visual MODFLOW Exercise: ChemWest 
 
 
 
 
 Open 
A window will appear highlighting any validation failures. This window should indicate that the 
starting and ending head values are below the cell bottom in 40 cells. To resolve this validation 
error we will delete the invalid cells. 
 Delete invalid cells from the menu shown in the window 
 Apply click the button next to the menu 
 Repeat for the remaining validation error 
You should now see a series of red dots in the upstream Norman River cells, indicating the 
presence of a constant head boundary condition. The final step in this process is to delete any 
boundary conditions in cells which do not actually fall under the Norman River. Specifically, 
many of the constant head boundary conditions in Column 12 (near the edge of the Norman 
River) should be removed. 
 Erase… from the Toolbox 
 Single from the menu that appears 
 Delete all constant head boundary conditions which are not located inside the 
Norman River 
When you’re finished deleting inappropriate boundary condition cells your model should look 
something like the image below: 
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Visual MODFLOW Exercise: ChemWest 
 
 
 
 
 
Similarly, create a constant head boundary condition for the below dam portion of the Norman 
River while taking note of the edge of the river bank. When creating the constant head to 
represent the Norman River, ensure that 587.5 ft is the Starting Head and Ending Head at the 
upstream cells, and 586.5 ft is the Starting Head and Ending Head at the downstream cell. 
NOTE: you will only have to copy the initial distribution of 
heads in column 1 six times (i.e. columns 1-7), since the 
Norman River is not as wide downsteam. 
When you’re finished assigning the constant head boundary condition downstream of the dam, 
the downstream are should look like the image below: 
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Visual MODFLOW Exercise: ChemWest 
 
 
 
 
 
At the end of this workflow, you should have two constant head boundary conditions, Constant 
Head 1 for the above-dam part of the Norman River and Constant Head 2 for the below-dam 
part of the Norman River. Please note that the names of these boundary conditions may be 
different, but you can simply rename them by right-clicking the object in the Model Explorer 
and selecting ‘Rename…’. 
Deer Creek 
Deer Creek drops from 598 ft just east of the main Highway, to 586.8 ft, where it flows into 
Norman River. The creek is 3 feet deep along its length, has a riverbed thickness of about 1 foot 
on average, as illustrated in the following figure. 
 
 
 
 
 
 
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Visual MODFLOW Exercise: ChemWest 
 
 
 
 
Deer Creek – Cross-sectional view 
 
 
 
 
 
 
 
 
The conductance of the Deer Creek “riverbed” will be calculated automatically using the 
following information: 
• Riverbed thickness; 
• Riverbed Kz (0.22 ft/day); 
• River width 
Let’s look at how we can insert this River as a Boundary Condition within our model. 
 River from the Toolbox drop down menu 
 [Zoom to Box] in order to zoom to a specific area in the model 
 Draw a rectangle around Deer Creek 
 
Now we need to map out a polyline to represent Deer Creek. 
El. 598 - 586.8 ft 
3 ft 
1 ft 
5 ft 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
River Bottom (Elevation) 
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Visual MODFLOW Exercise: ChemWest 
 
 
 
 
 Assign from the Toolbox menu 
 Polyline from the menu that appears 
 Draw a polyline overlapping the river by clicking multiple points along the line 
 Right click to close the Polyline 
 Finish 
This will open the Define Boundary Condition window. 
 Type: Deer Creek under Name 
 Next >> 
This will open the Boundary Condition parameter window: 
 
Based on the cross-sectional view of Deer Creek, we should be able to fill in the required 
information in this parameter window. We are going to use the ‘Interpolate’ functionality 
within Visual MODFLOW Flex to interpolate between the data points available for the river. By 
entering the required parameters, Visual MODFLOW Flex will automatically calculate 
conductance. 
Since we know the Deer Creek flows from the Main Highway into the Norman River, we are 
going to sort the cells in ascending order based on their column number (from smallest to 
largest). 
 to sort the cells from smallest column to largest 
 Type: 586.8 under River Stage (ft) in the top-most cell 
 Type: 582.8 under Riverbed Bottom (ft) in the top-most cell 
 Type: 598 under River Stage (ft) in the bottom-most cell 
 Type: 594 under Riverbed Bottom (ft) in the bottom-most cell 
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Visual MODFLOW Exercise: ChemWest 
 
 
 
 
Now we are going to use the interpolate function within Visual MODFLOW Flex to interpolate 
between the top and bottom cells of the Norman River. 
 While holding CTRL, select both the first and the last rows in the entire table 
 [Interpolate] to interpolate and provide a smooth transition in 
 head values upstream of the Norman River 
Let’s continue by filling in all the other constant parameter values. Enter the following values in 
the first row of the appropriate column, then use the ‘Assign to column’ ( ) button (or click 
F2) to assign values to all cells. 
 River Width (ft) = 5 ft 
 Riverbed Thickness (ft) = 1 ft 
 Riverbed Kz (ft/d) = 0.22 ft/d 
Ensure these values are assigned to all the cells of the Norman River. Based on these parameter 
values that are entered, Visual MODFLOW Flex will calculate a value for the Norman River 
Conductance. Your Define Boundary Condition window should now look similar to this: 
 
 Finish 
After clicking [Finish], you will notice that some of the river cells seem to disappear. In fact, the 
river cells have been assigned correctly according to the “Assign to appropriate layer” option. 
Check in another layer to see if you can find the other river cells. If it’s not clear why this has 
occurred, be sure to ask you instructor. 
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Visual MODFLOW Exercise: ChemWest 
 
 
 
 
Bass Lake and Salmon Pond 
We are going to assign Bass Lake and Salmon Pond as river boundaries. The pond elevations, 
ponds depths, “riverbed” thicknesses and Kz’s of Bass Lake and Salmon Pond are listed in the 
following table. You will be able to derive all the necessary parameters for assigning the River 
boundaries using these numbers. Check with your instructor to ensure that everything isentered correctly. 
 Pond Elev. 
(ft) 
Pond Depth 
(ft) 
Riverbed 
thickness (ft) 
Riverbed 
Conductivity 
(ft/day) 
Bass Lake 599 3 1.0 0.066 
Salmon Pond 599 3.5 1.0 0.066 
We you’re finished assigning the Bass Lake, Salmon Pond and Deer Creek boundaries your 
display should look similar to the image below (model Layer 1): 
 
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Visual MODFLOW Exercise: ChemWest 
 
 
 
 
2.11. Assigning Aquifer Recharge 
Average Annual Net Recharge 
The average annual net recharge across the site, based on analysis of historical data, is about 8 
inches. It is also estimated that flow originating from a portion of the uplands to the east 
contributes approximately an additional 15.5 inches of recharge per year. This recharge enters 
the aquifer along the interface between the shale bedrock and the sand and gravel aquifer. This 
additional recharge estimate, and how it was implemented in the model, is explained below. 
Estimate Recharge Contribution from the Uplands 
Using topographic mapping and low-altitude aerial photographs of the upland areas, 
topography that channels precipitation toward the aquifer was identified. Not all of the upland 
area was determined to contribute recharge due to the presence of surface water divides and 
closed catchments. In fact, only 10 percent of the total upland area was assessed to be suitable 
for channeling overland and interflow to the aquifer. 
The amount of recharge contributed by the upland areas was calculated based on the area 
calculations of the upland areas, and the annual recharge estimate for the region of 8 inches. 
These data were incorporated into the model following the steps shown below: 
A. Total Recharge = 2,537 ft3/day (area of catchments x net groundwater recharge) 
B. Area of Recharge Strip Assigned in the Model = (length of band x average cell width) 
= 11,000 x 65.2 ft = 717,200 ft2 
C. Total Recharge / Recharge Strip Area Specified in Model 
= 2,537 ft3/day / 717,200 ft2 = 3.53 x 10-3 ft/day = 15.5 inches/year. 
To implement this recharge zone in the model, create a recharge area along the interface of the 
shale bedrock and aquifer - one model cell wide - and assign an additional recharge of 15.5 
inches per year. The 15.5 inches per year is dependent upon the area of the recharge strip that 
you specify in the model. If the width of the strip changes, for example if you make it two cells 
wide instead of one, then the recharge value assigned in the model must be halved. 
Remember to add the 8 inches of ambient recharge to the cells in the strip for a total recharge 
rate of 23.5 inches/yr. 
 Layer: 1 ensure you are viewing model layer 1 
 Recharge from the dropdown menu under Toolbox 
 Assign 
 Entire Layer from the dropdown menu for Assign 
This will open the Define Boundary Condition window 
 Next >> to accept default name 
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Visual MODFLOW Exercise: ChemWest 
 
 
 
 
 Static from the dropdown menu for Schedule on the top 
 left in the Define Boundary Condition window 
 Type: 8 under Recharge (in/yr) 
 (or F2) to assign this value to the entire column 
 Type: 0 under Ponding (ft) 
 (or F2) to assign this value to the entire column 
 Finish 
Now we must assign a new recharge zone to represent the higher recharge area along the 
interface of the shale bedrock and aquifer at a one cell width using a polygon. 
 □ Recharge unselect this boundary condition in the Model Explorer 
 Assign under the Toolbox 
 Polygon 
 Draw a polygon with a one-cell width along the interface of the shale bedrock and 
 aquifer, as shown below 
 Right click once you are done drawing the polygon 
 Finish 
NOTE: it is not possible to ‘Zoom’ while the ‘Assign 
Polygon’ tool is being used, which may make it difficult to 
draw a polygon which properly identifies all the required 
cells. You may want to assign the cells along the higher 
recharge area in multiple ‘sections’. 
It is also possible to move the viewer window during the 
‘Assign Polygon’ tool is being used, by using the keyboard 
arrow buttons. 
This will open the Define Boundary Condition window. 
 Next >> 
 Static from the dropdown menu for Schedule on the top 
 left in the Define Boundary Condition window 
Similar to the Recharge boundary for the entire layer, assign the following values to the polygon 
constructed to represent Recharge Zone 2: 
 Recharge: 23.5 in/yr 
 Ponding: 0 ft 
Once you are done assigning Recharge Zone 2 to the model, the layer view should look similar 
to the image below. Furthermore, if you click the Database button under the Toolbox, this 
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Visual MODFLOW Exercise: ChemWest 
 
 
 
 
should open up the Recharge Zone summary for the model. Ensure that there only two zones in 
this window and if not, please ask your instructor for further help. 
 
2.12. Define Calibration Targets 
The monitored head levels used for contouring the water level in Task 3 must now be entered 
into the model as calibration points. Such calibration points can be imported from the excel file, 
calpts.xlsx, as follows: 
 Next Step proceed to the Select the Next Step step in 
 the workflow 
 to Define Observation Wells 
We are going the start by importing the observation well data into our Data Tree 
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Visual MODFLOW Exercise: ChemWest 
 
 
 
 
 Right Click in the Data Tree window 
 Import Data… from the menu that appears 
 Well from the dropdown menu for Data Type 
 calpts.xlsx from the Supporting Files directory 
 Type: Observation Wells under Name 
 Next >> 
 Next >> 
  Relative under the Time section 
  Well heads with the following data 
  Observation points 
  Observed heads 
 
 Next >> 
 Next >> 
This will bring you to the Data Mapping window and at this point we need to assign the 
appropriate source columns to their respective target fields. First, let’s begin by looking at the 
Well Heads tab: 
 Well Id: Well ID 
 X: X-coordinate (ft) 
 Y: Y-coordinate (ft) 
 Elevation: Elevation 
 Well Bottom: Well Bottom 
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Visual MODFLOW Exercise: ChemWest 
 
 
 
 
 
Next we will proceed to match the appropriate source columns to their respective target fields 
in the Observation Points tab: 
 Obs. Point Id: Screen ID 
 Obs. Point Z: Screen Elevation 
 Observed Head: Head (ft) 
 Observation time: Observation Time (day) 
 Head observation date unit category: None 
 
 Next >> to preview the imported data 
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Visual MODFLOW Exercise: ChemWest 
 
 
 
 
 Finish to finally import the data 
Once the observation data has been successfully imported, the icon will appear in the Data 
Tree of the project. In addition, you should add the following monitoring point by accessing the 
observation data table in Visual MODFLOW Flex. 
Well Name 
X-
Coord 
Y-
Coord 
Elev. 
Well 
Bottom 
Screen 
ID 
Screen 
Elev. 
Obs. 
Time 
Head 
34 
(entered 
automatically) 
3304 4755 630 0 A 590 1/2/2017 602.22 
Let’s begin by opening the Observation Well data table. 
 Right click ‘Observation Wells’ in the Data Tree 
 View Spreadsheet from the dropdown menu 
This should open the TableView window with the list of all the imported observation wells 
data. 
 under the Well Heads tab in the TableView window 
This will add a row to the Well Heads tab and we can enter the following information from the 
table above: X-coordinate, Y-coordinate, Zmax (Elevation) and Zmin (Well Bottom). 
Next, lets add the Observation Data for this associated well: 
 under the Observation Points tab to enter the Screen ID 
 and elevation 
 under the Observation Data tab to enter the Observation 
 date and Observed Head 
In the end, the TableView window should look similar to this: 
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Visual MODFLOW Exercise: ChemWest 
 
 
 
 
 
 Apply 
 OK 
Now let’s bring these observation points into the model. 
 Click on ‘Observation Wells’ in the Data Tree to highlight the data set 
 under Select Observation Object in the Toolbox 
This will bring the observation points in the model and this can be seen in the Model Explorer 
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Visual MODFLOW Exercise: ChemWest 
 
 
 
 
 
To see the distribution of observation wells used for calibration simply activate the ‘Heads 
Observations’ item in the Model Explorer and view model layers 2 and 3. 
2.13. Assign Zone Budget Zones to Deer Creek 
Zone Budget is a tool for measuring the flow from one part of the model to another. In this task 
you are given stream flow measurements from two locations in Deer Creek. The difference 
between these flow measurements is the net baseflow to the stream, assuming evaporative 
losses are negligible. 
NOTE: Baseflow measurements are an excellent added 
calibration target as they allow you to calibrate to a flow 
rate as well as a head distribution, which greatly increases 
the uniqueness of the model solution. 
In this task, you will use Zone Budget to create a base flow measurement zone along Deer 
Creek, between the two stream gauging stations. Zone Budget allows a measurement of the 
gain or loss of stream flow. Later, you will compare the measured and predicted base flow 
values to improve your model calibration. 
The two stream gauging stations located along Deer Creek are indicted by a diamond symbol on 
the base map. The measured streamflow at the lower station was about 27,698 ft3/day and at 
the upper station it was 14,326 ft3/day. 
 
 
 
 
 
Upstream 
station 
 
 
 
 
 
 
 
 
 
 
Downstream 
station 
 
 
 
 
 
 
27,698 ft3/day 
 
 
 
 
 
 
 
 
 
 
 
14,326 ft3/day 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Net gain to groundwater (note that 
some reaches between the two 
stations may gain, others may lose) 
 
 
 
 
 
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Visual MODFLOW Exercise: ChemWest 
 
 
 
 
The difference between these two numbers represents the river gain of water coming from the 
groundwater system and can be compared with the flow across the river boundary calculated 
by ZoneBudget. To facilitate this calculation, you’ll now define a zone along Deer Creek. 
To define a Zone Budget Zone: 
 Define Zone Budget Zones from the Numerical modelling workflow 
  BaseMap in the Data Tree window 
  Deer Creek from the Model Explorer under Boundary 
 Conditions > Rivers 
This will turn on the basemap and the river boundary condition that we will use as a reference 
to assign zones in ZoneBudget. Make sure you are currently viewing the model in Layer 1. 
 to zoom into the Deer Creek area of the model 
 Draw a rectangle covering the active area of Deer Creek 
 Assign under Toolbox 
 Single to assign individual cells to the desired Zone 
 Click on the visible Deer Creek river cells in Layer 1 of the model domain which fall 
between the two river gauge stations 
NOTE: we are primarily interested in the stretch of creek 
between the flow gauges, since this will provide us with 
some information to help us calibrate/validate our model. 
In other situations you may be interested in the entire river 
stretch, in which case you would extend this new zone 
along the remaining cells which represent Deer Creek. 
 
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Visual MODFLOW Exercise: ChemWest 
 
 
 
 
 Finish 
This will open up the ‘Create New Zone Budget Zone’ window. 
 New to create a new zone, Zone 2 within Zone Budget 
  Layer 1 to assign this zone to Layer 1 cells 
 OK 
This will highlight the cells that have been assigned to Zone 2 in Layer 1. 
 
Similarly, switch to Layer 2 and assign the remaining Deer Creek river cells between the gauges 
to Zone 2 for the Zone Budget analysis. When you have completed assigning Zone 2, you should 
have 2 Zonebudget zones, Zone 2 (blue) which represents the stretch of creek between the 
gauges, and Zone 1 (white) which represents the rest of the model domain while the green area 
represents the inactive zones in the model domain. 
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Visual MODFLOW Exercise: ChemWest 
 
 
 
 
PART 3: CALIBRATION 
Calibration is the process of modifying the input model parameters until the model results 
reasonably match actual site conditions. In this lab, you will calibrate your model to measured 
water level values and stream base flow from Deer Creek. Finally, you should always validate 
your results against an independent set of data, such as water levels during a different season 
or a transient pumping test. 
3.1. Run and calibrate the model 
Before running the model, we need to assign a uniform Initial Heads value to the entire model. 
We are going to change the default initial heads value to 593 ft. This value will be used for 
every cell in the model. Later, after you have started running and calibrating your model, you 
may want to import your initial heads from a previous MODFLOW run. This can drastically 
reduce the amount of time required for the solution to converge. 
 Define Properties from the numerical modeling workflow 
 Initial Heads from the dropdown menu under Toolbox 
 Edit … to access the database values for Initial heads 
This will open the Edit property window and here we can change the Initial Heads (ft) value 
from 100 ft to 593 ft and assign it to all the cells in the model. 
 Type: 593 under Initial Heads (ft) 
 (or F2) to assign this value to the entire column 
 OK to close the Edit Boundary window 
 Select Run Type from the numerical modeling workflow 
 to proceed to select the engines for the model run 
 MODFLOW-2005 from the menu under Flow Engine 
 □ Run Transport Engine do NOT run transport engines at this stage 
  ZONEBUDGET to run the Zone Budget with MODFLOW-2005 
 Next Step 
This will bring you to the Translate workflow step: 
 Settings under MODFLOW-2005 nodes 
 BCF6 (Block Centred Flow) from the dropdown list for Property Package 
 Steady-State from the dropdown list for Run Type 
 Type: 18250 for the Steady-State Simulation Time 
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Visual MODFLOW Exercise: ChemWest 
 
 
 
 
 Solvers under MODFLOW-2005 nodes 
 Type: 0.001 for Head change criterion (HCLOSE) 
 Type: 0.001 for Residual criterion (RCLOSE) 
 Type: 0.75 for Damping factor (DAMP/DUMPPCG) 
A lower damping factor reduces the aggressiveness of the solver and will reduce the tendency 
of the solver to oscillate. Finally, activate the re-wetting package in the model: 
 Rewetting 
 Active from the menu for Cell wetting (IWDFLG) 
Now, let’s go ahead and, translate and run our model engine package: 
 to tranlate the engine packages 
 Yes for the Warning regarding Initial Head being below 
 bottom of Layer 1 
Finally, you should see ##ZONE BUDGET Translation Finished## and ##Translation Finished## 
messages in the Translation Log window. 
 Next Step 
 to run MODFLOW-2005 and ZONEBUDGET 
Once the engines are done running, depending on the combination of hydraulic conductivities 
you specified, your model will be more or less similar to the measured heads. 
Be aware that your model may not converge the first time you run the model. However, do not 
be discouraged - this is a typical intermediate step in building a working groundwater flow 
model. 
If your model does not converge, go back to the Input Module and review the properties and 
boundary conditions you entered for consistency and reasonableness. 
3.2. Calibration Statistics 
When your model has converged, you will be able to assess its ability to calculate a head 
distribution that matches actual site head data. Perhaps the most common way to 
quantitativelyassess your model’s degree of calibration is to plot the calculated head 
distribution versus observed head distribution using observation points which you place in your 
model. To view a plot of Calculated Head versus Observed Head for your model: 
 Next Step 
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Visual MODFLOW Exercise: ChemWest 
 
 
 
 
 to view plot of Observed vs Calculated Heads 
This should open up an empty chart. Let’s go ahead and selected ALL available values to be 
plotted on the scatter plot: 
  All Times under Observations 
  All Obs. under Observations 
 Apply to plot all Observed vs Calculated heads 
Using the following guidelines, examine your Calculated Head versus Observed Head plot. The 
figure below illustrates a calibrated heads plot: 
 
Do your measured versus calculated heads meet the less than 10 percent normalized root 
mean square (RMS) error calibration criterion? 
An acceptable RMS value for this model is less than 1.0 ft or a Normalized (i.e., scaled) RMS of 
less than 10%, which is calculated as follows: 
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Visual MODFLOW Exercise: ChemWest 
 
 
 
 
Normalized RMS = RMS 
 the maximum head change across the model domain 
Remember, Visual MODFLOW Flex calculates the Normalized RMS based on the global 
difference in head elevations across the model. In a regional model with considerable relief, it 
may be more appropriate to define a local Scaled RMS for areas of particular interest. If the 
normalized RMS criterion is satisfied, are there any points in the model that are not calibrated? 
If so, are these non-calibrated areas of the model important to the project? If they are, examine 
your model in those areas and consider adjusting the input parameters to achieve a better 
calibration result. 
In the ChemWest model, we have a single flow measurement for comparison. To compare the 
measured flow to/from Deer Creek to that calculated by Zone Budget engine: 
 Zone Budget in the top left corner of the View Charts window 
This will open the Zone Budget MODFLOW viewer window with the various windows open for 
Percent Discrepancy, In-Out, Time-Series and Time Step as seen below: 
 
To examine the amount of groundwater flow between the stream and the aquifer system, click 
on the Time Step window in the Zone Budget window. 
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Visual MODFLOW Exercise: ChemWest 
 
 
 
 
 
In order to see the actual values for the rates in ft3/day, we just need to click on each of the 
bars. Let’s look at the Zone Budget calculations for Zone 2: 
 click the down button to switch to Zone 2 
 Click on the bars for River Leakage in the window to display exact values 
 
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Visual MODFLOW Exercise: ChemWest 
 
 
 
 
In the screen capture above, you will see the following results: 
• River leakage into the aquifer: 0 ft3/day 
• River leakage out of the aquifer: 13,704 ft3/day 
The exact magnitude of your numbers will be different from the ones given here because your 
model will be different. These results indicate that Deer Creek is gaining water all along this 
reach (river leakage out of the aquifer) but not losing water (river leakage into the aquifer). 
 
 
 
 
 
 
 
 
 
 
 
 
 
This terminology can be a confusing point so check with your instructor if you have any 
questions. The net flow across the river boundary is calculated as follows: 
 Net Flow Across River Boundary = Input River Leakage – Output River Leakage 
 = 0 – 14,641 ft3/day 
 = -14,641 ft3/day 
A negative result indicates a net loss of water from the aquifer to Deer Creek because all flow 
rates in MODFLOW are considered with respect to the aquifer. Compare these calculated 
results with the difference in streamflow you calculated earlier in this exercise. 
ZoneBudget output is viewed in graphical format, which is very handy for a quick overview of 
relative magnitudes. Let’s go ahead and complete displaying the values for Zone Budget 
calculations for both Zone 1 and Zone 2: 
“losing stream” 
= input “river leakage” 
= positive “river leakage” 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
“gaining stream” 
= output “river leakage” 
= negative “river leakage” 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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If your model meets the quantitative calibration criterion, do not assume your model is ready 
for use in making predictive simulations. An important part of the calibration process is a 
qualitative review of the model results – that is, are the model results reasonable based on 
your experience and knowledge of the region? Specifically, do the head contours and 
contaminant-plume geometry agree qualitatively with the modeled results? To conduct such a 
qualitative comparison, you may want to digitize hand-contoured isopleths (concentration 
contours) and hydraulic heads/water table. These digitized plots can be imported to Visual 
MODFLOW Flex as a .DXF file and overlain on the calculated results for comparison. 
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Visual MODFLOW Exercise: ChemWest 
 
 
 
 
PART 4: TRANSPORT SIMULATION SET-UP 
4.1. Introduction 
The remaining sections of the lab illustrate how a model can be used to help decide whether 
pre-emptive remedial measures are required at a site where potential contaminant sources 
exist. Let us suppose that the owners knew of the possibility of BTEX contamination within their 
site. This led them to hire a specialist to estimate the parameters that would be required to 
develop a model. A review of the literature indicated that a longitudinal dispersivity of 16 ft 
would be appropriate for this type of depositional environment and the potential size of the 
plume at this site. The ratios of transverse to longitudinal dispersivity, and vertical to 
longitudinal dispersivity were estimated at 0.1 and 0.01, respectively. The bulk density was 
estimated at 106 lb/ft3. A series of batch tests were conducted and a linear Kd of 3.0210-11 
L/g was determined for these aquifer materials for the range of expected concentrations. 
Finally, a first-order decay constant of 0.0005 day-1 was estimated as the most optimistic 
scenario for natural attenuation of BTEX at this site. Although decay of the sorbed phase 
sometimes occurs, it is conservatively assumed not to occur at this site. Using these 
parameters, we will construct a series of three transport scenarios to help decide whether an 
engineered remediation system is likely to be required. In summary, the parameters are as 
follows: 
• l = 16 ft 
• t/l = 0.1 
• v/l = 0.01 
• Kd = 3.0210-11 L/g 
• b = 106 lb/ft3 
• aq = 0.0005 day-1 
• sorbed = 0 
We recommend that you read this section and the next section to gain an overall 
understanding before proceeding any further. 
4.2. Basic Parameters and Transport Boundaries 
If you are satisfied with the calibration of your flow model, you can use the results to conduct 
predictive simulations to identify the effect of a variety of remedial actions on the dissolved-
benzene plume at the site. You can now close the ZoneBudget results and return to the 
numerical modeling workflow, where you will define transport related parameters and 
boundary conditions. 
 Close the Zone Budget window 
 Define Properties from the numerical modelling workflow 
 Longitudinal Dispersion from the dropdown menu under Toolbox 
 Edit … to access the database values 
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Visual MODFLOW Exercise: ChemWest 
 
 
 
 
This will open the Edit Property window for Longitudinal Dispersion. Let’s go ahead and change 
the longitudinal dispersivity from 10 ft to 16 ft. 
 Type: 16 in the first cell under the Dispersioncolumn 
 (or F2) to assign this value to the entire column 
Now all the cells in the model domain should have a Longitudinal Dispersivity value of 16ft. 
 
 OK 
Let’s go ahead and check the horizontal/longitudinal and vertical/longitudinal dispersivity ratios 
for the model. 
 Right-click Longitudinal Dispersion in the Model Explorer window under 
 RefinedChemwest > Run2 > Inputs > Properties > 
 Transport 
 Dispersion Parameters from the dropdown menu 
This will open the Dispersion Parameters window. For each layer of the model, ensure that the 
Horiz/Long and Verti/Long ratios are set to 0.1 and 0.01, respectively. 
 OK 
We need to go back to the engine setup in order to edit some of the transport settings. 
 Define Modeling Objectives from the numerical modelling workflow 
 Linear isotherm from the dropdown list for Retardation Model 
 Yes to dismiss any warnings 
 Type: Benzene for the Parameter Name under Species Parameter 
 Type: 3.02E-11 under Kd [1/(µg/L)] for the distribution coefficient 
 Model Parameters from the tabs available for the MT3DMS engine 
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Visual MODFLOW Exercise: ChemWest 
 
 
 
 
Type: 1700 for the Bulk Density (kg/m3) value 
Next, return to the boundary conditions and enter the contaminant source concentration in the 
location shown in the figure below. 
 Define Boundary Conditions from the Numerical modelling workflow 
 Constant Concentration from the dropdown menu under Toolbox 
 Type: 2 into the Layer 
 from the Viewer toolbar 
 Draw a rectangle in the upper middle portion of the site, as shown below 
Your view should now look something like this: 
 
Let’s add two benzene sources to Layer 2 of the model as constant concentration sources, with 
a concentration 2000 µg/L. Try and approximate the location of these two sources to the best 
of your abilities. 
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Visual MODFLOW Exercise: ChemWest 
 
 
 
 
 
 Assign under Toolbox 
 Polygon 
 Draw the first polygon with the 4 corners 
 Double-click to close the first polygon 
 Draw the second polygon with the 4 corners 
 Right-click and select finish 
This will open the Define Boundary Condition window: 
 Next >> to accept default name 
 Type: 2000 under Benzene (µg/L) 
 (or F2) to assign this value to the entire column 
 Finish 
This will highlight the cells that have been assigned a Constant Concentration value of 2000 
µg/L. If the cells are being assign as circles with a very neutral colour, we can change this by 
accessing the settings for the boundary condition. 
 Right click Constant Concentration 1 in the Model Explorer under Refined Chemwest > 
Run2 > Inputs > Boundary Conditions > Constant Concentrations 
 Settings from the dropdown menu 
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Visual MODFLOW Exercise: ChemWest 
 
 
 
 
This will open the Settings window for Constant Concentration 1. 
 Style from the available nodes on the left side 
 to change the colour of the symbol to Orange 
 OK 
 Square from the dropdown list for Symbol 
 Type: 4 under Size 
 Apply 
 OK 
Now your view should look similar to the one above. If not, please ask your instructor for 
assistance before proceeding any further. 
4.3. Inactive-for-Transport Region 
In some circumstances, making part of the model domain inactive with respect to contaminant 
transport can significantly reduce the simulation time. MT3DMS calculates the maximum 
allowable time step based on numerical stability criteria minimized across the model. The cell 
with the fastest travel time across it will dominate the selection of the transport time step. 
Thus, one small cell with a high groundwater velocity can be responsible for a very small 
MT3DMS calculated maximum time step. 
NOTE: If your time step is exceedingly small, your model 
may contain an inadvertently added grid line with a very 
small grid spacing. 
If the time step controlling cells are located outside of your area of interest for contaminant 
transport, then you have the option of specifying an area of the model as inactive for transport. 
In this particular model, the time step is controlled by the flow around the dam, which 
unfortunately is in our area of interest. Next figure shows approximately the area that should 
be considered inactive. Don’t forget to copy the inactive transport area to the other layers. 
© Waterloo Hydrogeologic Page 68 
Visual MODFLOW Exercise: ChemWest 
 
 
 
 
 
4.4. Concentration Observation Wells 
Now import a set of concentration observation wells so that breakthrough curves of the results 
can be plotted. This feature is useful for estimating the breakthrough time of critical 
concentrations, such as the drinking water limit, and for comparing multiple remediation 
scenarios. 
 Define Observation Wells from the numerical modelling workflow 
Then import the observation wells contained in conpts.xlsx as Concentration Observation Wells 
similar to how we imported the head observation wells however, make sure the import 
settings are for Observed Concentrations. This file does not contain any observed 
concentrations but it will provide the coordinates and screen elevations for plotting the 
modeling results. 
NOTE: the data mapping step during this import will 
require you to map the fields under the ‘Observation 
Points’ tab as shown below. These data will NOT be 
automatically mapped. 
 Obs. Point Id: Screen ID 
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Visual MODFLOW Exercise: ChemWest 
 
 
 
 
 Obs. Point Z: Screen Elevation 
 Chemical: Chemical Name 
 Concentration: Concentration 
 Concentration observation date: Observation Time 
The Observation Points tab should look similar to this: 
 
 Concentration Observation Wells in the Data Tree window 
 to bring the concentration observation data points 
 into the model 
This should create a Concentration Observations node in the Model Explorer. 
4.5. Solution Method and Output Times 
 Select Run Type 
 to proceed to select the engines for the model run 
  MODFLOW-2005 
  Run Transport Engine (MT3DMS) 
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Visual MODFLOW Exercise: ChemWest 
 
 
 
 
  ZONEBUDGET 
 Next Step 
In the Engine Settings window, we are going to keep the MODFLOW-2005 engine settings the 
same however, we do need to make changes to the MT3DMS Settings, Solution Method and 
Output Control. 
 General under the MT3DMS node 
 Total from the dropdown list for Porosity Options 
 Solution Method under the MT3DMS node 
 Yes in order Use Implicit GCG Solver 
 Output Control under the MT3DMS node 
 Type: 18250 for the Simulation time length (project time units) 
 Type: 100,000 for the Max number of transport steps 
 Output Times under the Output Control node 
 to add a row under the Output Times 
 additionally 11 time to get a total of 12 rows 
 Type the following values in each row: 365, 730, 1825, 3650, 5475, 7300, 9125, 10950, 
12775, 14600, 16475, 18250 
Now the window should look similar to this: 
 
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Visual MODFLOW Exercise: ChemWest 
 
 
 
 
While it is unlikely that you would present the results from all of these times, it is useful to have 
the additional output if you want to develop an animated presentation of your results. 
Before running one of the following three scenarios with MT3DMS, please refer to the following 
checklist to ensure you have correctly set up your model and are ready for the transport phase 
of the exercise: 
✓ Your flow model is reasonably calibrated based on the calibration criteria outlined 
earlier in this lab. If not, then please notify your instructor, who can subsequently 
provide you with a calibrated version of the model for the purposes of the following 
transport scenarios 
✓ You have selected theMT3DMS numeric engine, and specified the UFD advection 
method and the correct output time steps 
✓ You have specified a 50-year simulation length and 100,000 transport steps 
✓ The output times are specified 
✓ You have assigned two constant concentration sources of 2000 g/L to Layer 2 of 
your model 
✓ If you have completed the tasks from the list above, then you are now ready to run 
the transport section of this exercise 
4.6. Transport Scenarios 
You will now create a series of three transport runs. Let’s create a total of 3 runs: 
 Right click Run2 in the Model Explorer 
 Clone Model Run to create Run3 
 Right click Run2 in the Model Explorer 
 Clone Model Run to create Run4 
Once you’ve cloned the model you should have a total of three runs in the Model Explorer 
window, under the RefinedChemWest grid: Run2, Run3 and Run4. 
4.6.1. Run2 – Transport with adsorption only; no bioremediation or pump-and-treat 
This is a conservative scenario that will identify the potential for contamination of receptors 
downgradient of the site if no pumping well is installed and the contaminants are not naturally 
attenuated. Run the simulation as you have set it up and then compare the results to those 
obtained by Run3 and Run4. When viewing the Maps for the results, ensure you are in Layer 2 
since that is the layer we assigned the two constant concentration sources to. 
See Figures C8 to C12 in Appendix C for examples of results using the Upstream Finite 
Difference Method. 
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Visual MODFLOW Exercise: ChemWest 
 
 
 
 
4.6.2. Run3 – Same as Run2 plus a 50-GPM pump-and-treat system 
In order to open the related workflow for Run3: 
 Right click Run3 in the Model Explorer window 
 Open Related Workflow(s) from the dropdown menu 
This should open a new tab for RefinedChemwest – Run3. For this run, add a well at the 
location specified as the recovery well (approximately at X=2925, Y=4155) on the background 
map as a boundary condition. The well should be screened across the full thickness of the sand 
and gravel aquifer, i.e., layers 2 and 3 (606.15 ft to 557.887 ft), with an extraction rate of 50 
GPM specified. 
NOTE: To simulate an extraction well, should the pumping 
rate be negative or positive? The pumping rate should be 
negative, since an extraction well removes water from the 
aquifer. By convention, all flow rates in MODFLOW are 
considered with respect to the aquifer. 
Run the simulation and then compare the results to those obtained by Scenario A. MODFLOW 
must be executed before MT3DMS because you are now simulating the effect of a pumping 
well. See Figures C13 to C17 in Appendix C for examples of results. 
4.6.3. Run4 – Same as Run2 plus first-order decay (natural attenuation) 
Open a related workflow for Run4. Return to Define Modeling Objectives. 
 Linear isotherm from the dropdown menu for Sorption 
 First-order irreversible decay from the dropdown menu for Reactions 
 Yes to dismiss the warning 
Under the Species Parameters tab, enter the following values: 
 Type: 3.02E-11 [1/g/L] under Kd for the sorption coefficient 
 Type: 0.0005/day under K_mobile for the dissolved phase 
 reaction rate constant 
 Type: 0.0/day under K_sorbed for the sorbed phase reaction rate 
 constant 
Run the model and then compare the results to those obtained by Run2 and Run3. Figures C18 
to C22 in Appendix C illustrate examples of results plotted in plan. 
4.7. Comparison of Remedial Options 
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Visual MODFLOW Exercise: ChemWest 
 
 
 
 
4.7.1. Remedial Objectives 
When the transport simulations are complete, you can compare the results to help assess 
whether natural attenuation is likely to meet the objectives or whether an engineered system is 
required. The objectives at this site are to maintain benzene concentrations below certain 
criteria for a period of 50 years after any benzene leakage occurs as follows: 
<500 g/L at MW-10 and MW-33 
<5 g/L (the drinking water limit) at MW-73 and MW-15 
<1 g/L at MW-7, MW-70 and 77south. 
NOTE: The grid spacing in this model is much too coarse to 
be assessing downgradient concentrations that are so 
much lower than the source concentration. An actual 
assessment would require a much finer grid and an 
assessment of numerical error. 
Remember to check all layers when conducting your assessment. In the end, what are your 
conclusions: 
• If benzene is not degrading naturally in the field, are the water-quality objectives met? 
• If benzene is degrading naturally in the field, is an engineered pumping system 
required? 
• Will the proposed pumping system be sufficient if benzene is not degrading naturally? 
• What design modifications would you propose to increase the effectiveness of the 
pumping system? 
• Do you think that the current network of concentration monitoring wells will adequately 
characterize the predicted plume geometry? How would this influence your conclusions 
about whether the objectives are being met? 
Compare your conclusions with those of other participants in the course to see if they differ. 
This will give you some insight into the variability of modeling results given the same set of field 
data. The following sections describe some additional tools within Visual MODFLOW that will 
help you conduct your assessment. 
4.7.2. Visualizing Results as Breakthrough Curves 
Besides plotting concentrations in plan, breakthrough curves are also useful for depicting the 
effect of different remediation techniques and especially for comparing the results of several 
techniques. One of the advantages of breakthrough curves is that a calculated result is provided 
for each time step in the simulation rather than the limited number of output times that you 
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Visual MODFLOW Exercise: ChemWest 
 
 
 
 
specify for all grid cells. This makes it easier to identify the calculated breakthrough time of a 
target concentration, such as the drinking water limit. An example of a breakthrough curve is 
illustrated in the following screen capture. 
 
Breakthrough curves can be plotted for any of the concentration observation wells. The 
modeling results can be exported using the button from the top menu. This allows you 
to export the curve in a .csv file format that can be opened in Microsoft Excel. 
4.7.3. Visualizing Model Results in 3D 
Viewing the modeling results in three dimensions often helps to gain insight into the transport 
and attenuation processes at a site and the effects of various remedial options. For example, 
the following techniques can be very useful: 
▪ Arbitrary horizontal slices through the model domain; 
▪ Vertical cross-sections along or perpendicular to a flowline; 
▪ Vertical cross-sections through a set of environmental receptors, (e.g. water wells); 
▪ Three-dimensional iso-surfaces. 
These types of views allow the hydrogeologist to examine the results in a way that is most 
relevant to the purpose of the analysis. Furthermore, two and three-dimensional animation 
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Visual MODFLOW Exercise: ChemWest 
 
 
 
 
techniques can be useful for illustrating time-dependent processes such as contaminant 
transport or water-table drawdown. This section of the lab will familiarize you with some 
techniques for assessing your transport modeling results in three dimensions. 
You will create a 3D volumetric representation of the contaminant plume within the model 
domain by creating an isosurface for a selected concentration value. To recreate the images 
below ensure that you are displaying results for model Run2. 
 Right click Run3 in the Model Explorer window 
 Open Related Workflow(s) from the dropdown menu 
 View Maps go to the View Maps workflow step 
  3D from the Views window to activate the 3D viewer 
  Concentration (Benzene) from the Model Explorer underRun2 
The main tools for orienting the model image are located at the top of the viewer window. The 
model view can be rotated by holding down left click on the mouse and rotating the view. 
You can access the display settings for each output node be enabling it and right clicking and 
accessing Settings. This will open the window to adjust formatting, isolines, slices, colormaps 
and isosurfaces. 
Once you have briefly explored the various features of the 3D Explorer, rotate the image to 
produce a view similar to the figure below (which shows the site map, water table (semi-
transparent) and benzene concentrations (as isolines)): 
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Visual MODFLOW Exercise: ChemWest 
 
 
 
 
 
NOTE: For printing purposes, the background and frame 
colour has been changed from black to white. (These 
colours can be modified by right clicking the viewer 
window and selecting background color) 
To view a horizontal slice of the simulated contaminant plume, select Concentration (Benzene) 
from the Project Tree. Right-click and select Settings from the pop-up window that appears. 
From the Style/Colormap node, select Show Colormap. Then, select a Layer slice type and enter 
a Layer Number of 2. 
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Visual MODFLOW Exercise: ChemWest 
 
 
 
 
 
You can also display an animated image of the plume by accessing Animation parameters by 
Right-clicking in the 3D View window. This will give you the option to either rotate the model or 
create a transient animation over a certain period of time. 
You may wish to zoom in on the area of interest, and turn on additional model properties. 
 
This concludes the ChemWest Exercise. 
© Waterloo Hydrogeologic 
Visual MODFLOW Flex Exercise: Valley 
Calibration Using PEST Run 
Problem Description 
This exercise is designed to lead you through the calibration of a two-dimensional groundwater 
flow model using the popular parameter estimation program PEST. In this exercise, you will: 
• open and inspect an existing model, 
• attempt to calibrate the model manually; and 
• use PEST to calibrate your model. 
Terms and Notations 
For the purposes of this tutorial, the following terms and notations will be used. (This assumes 
you are using a right-handed mouse.) 
type - type in the given word or value 
 - press the <Enter> key 
 - click the left mouse button where indicated 
 - double-click the left mouse button where indicated 
Starting Visual MODFLOW Flex 
On your Windows desktop, you will see an icon for Visual MODFLOW Flex 
 Visual MODFLOW Flex to start the program. 
The following Visual MODFLOW Flex window will appear: 
 
Visual MODFLOW Flex Exercise: Valley 
 
© Waterloo Hydrogeologic Page 2 
PART 1: INSPECTING THE VISUAL MODFLOW MODEL 
A set of Visual MODFLOW files for this model has been supplied. Start Visual MODFLOW Flex and 
open the Visual MODFLOW Flex file Valley_start.amd. 
 File / Open Project… to open the project 
 Browse to the location where you downloaded the 
 ‘Supporting Files’ folder 
 Valley_start.amd select this file 
 Open 
Note: By default, new Visual MODFLOW Flex projects will 
be saved to the following location - 
[C:\Users\<username>\Documents\Visual MODFLOW 
Flex\Projects] 
When the Valley project opens you will see the following display: 
 
The display shows the Define Modeling Objectives step in the numerical modelling workflow. 
Please note that this exercise is focused on the use of the PEST module. For that reason the 
Visual MODFLOW Flex Exercise: Valley 
 
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majority of work to configure the numerical model has already been completed. As you can see 
from the workflow tree, the majority of steps in the numerical modelling workflow are already 
green and show a checkmark, indicating that these steps have been completed: 
 
Before we proceed to the execution of our PEST model, let's spend some time familiarizing 
ourselves with the model configuration. We can do this by moving through the different steps in 
the numerical modeling workflow. Let’s proceed to the View/Edit Grid step: 
 [Next Step] proceed to the next step in the workflow 
 [Next Step] proceed again 
 [Next Step] click third time to arrive at the View/Edit Grid step 
OR 
 View/Edit Grid click this directly from the workflow tree to 
 proceed immediately to the selected step 
1.1 Review Model Structure/Grid 
When you arrive at the View/Edit Grid step your display will look like the image below. This stage 
of the workflow allows you to review your finite difference grid and determine if any grid edits 
are required (e.g. refinement around areas of interest). 
Visual MODFLOW Flex Exercise: Valley 
 
© Waterloo Hydrogeologic Page 4 
 
The finite difference grid is superimposed over the model domain. All cells are 6.25 m wide (rows) 
and 5 m high (columns). You can view cell dimensions in the Grid Editor: 
 Edit grid from the Toolbox under Grid Refinement 
And the Edit Grid window will appear, as shown in the image below. This window allows you to 
apply grid refinements along a range of rows/columns. The bottom left corner of this window 
also displays the minimum/maximum cell dimensions for your grid. If a grid edit is applied then 
the model cells will not have a uniform width/thickness. In this case please note that the 
individual cell dimensions are listed along the bottom of the viewer in both the Edit Grid window 
and also the regular VMOD Flex interface. Click Cancel to exit this window after reviewing. 
Visual MODFLOW Flex Exercise: Valley 
 
© Waterloo Hydrogeologic Page 5 
 
 
 Cancel 
Take a moment to review the Row or Column view when you’re back on the View/Edit Grid 
workflow step. 
  Row (or Column) from the Views frame 
The Viewer display should look something like the image below: 
Visual MODFLOW Flex Exercise: Valley 
 
© Waterloo Hydrogeologic Page 6 
 
As you can see, there is only one layer in this relatively simple model. Let’s deactivate the 
row/column view, and proceed to the next step in our workflow. 
 □ Row (or Column) from the Views frame, to remove the view 
 [Next Step] proceed to the next step in the workflow 
1.2 Review Model Properties 
Let’s take a moment to review the flow properties that have been defined for this model (e.g. 
hydraulic conductivity, storage coefficients, porosity, etc.). The valley alluvium is divided into 
three zones. When you arrive at the Define Properties step in the workflow your display will look 
like the image below: 
Visual MODFLOW Flex Exercise: Valley 
 
© Waterloo Hydrogeologic Page 7 
 
As you can see, there are three property zones within this groundwater model. The model has 
three hydraulic conductivity zones (K1, K2 and K3) and three storage zones (Sy1, Sy2, and Sy3). 
The three zones currently have homogeneous conductivity and specific yield values. These values 
should be verified by accessing the model properties: 
 Conductivity from the dropdown menu under Toolbox 
 Edit… under Toolbox, to access the database for 
 Conductivity 
This will open the Edit Property window, as shown below: 
Visual MODFLOW Flex Exercise: Valley 
 
© Waterloo Hydrogeologic Page 8 
 
From the Zone table shown on the left of the Edit Property window click on Zone 1, then Zone 2 
and then Zone 3. Ensure that all three zones have the same hydraulic conductivity property values 
(i.e. Kx = 2 m/d, Ky = 10 m/d, Kz = 10m/d). 
 Cancel to close the Edit Property window 
Next, verify three storage zones, the same way you did with the hydraulic conductivity zones: 
 Storage from the dropdown menu under Toolbox 
 Edit under Toolbox, to access the database for Storage 
This will open the Edit Property window and you verify the storage and porosity values. Please 
note that the stree property zones do have different values for specificstorage (Ss), effective 
porosity (Ep) and total porosity (Tp), which are all defined in the storage properties file. Take a 
moment to review these properties: 
Visual MODFLOW Flex Exercise: Valley 
 
© Waterloo Hydrogeologic Page 9 
 
 Cancel to close the Edit Property window 
Note that Kx is the only hydraulic conductivity parameter being used. In this model, anisotropy is 
controlled by the anisotropy factor, so let’s ensure that the ratio between Ky and Kx is 1. So Ky is 
not required; the model is 2D so Kz is not required. 
 Translate click this directly from the workflow tree to 
 proceed immediately to the selected step 
 Anisotropy under MODFLOW-2005 under the Settings tab 
 Anisotropy By Layer select this option from the list menu for Anisotropy 
 Factor 
Ensure that under Layer 1 that the Ky/Kx Ratio is 1. 
Also note that neither Ss nor porosity are used in this calibration. Ss is used only for confined 
layers, and this model has only one unconfined layer. The effective porosity (Ep) is used for 
MODPATH particle tracking, and the total porosity (Tp) is used in the MT3DMS calculations – 
neither of these programs are used in this exercise. 
1.3 Review Boundary Conditions: Wells, Constant Head and Recharge 
Let’s take some time to review the boundary conditions that have been applied to this model. 
We’ll start with the distribution of pumping wells. 
To inspect the wells, we’ll return to the Define Properties workflow step, and then make the 
various boundary conditions visible by selecting them in the Model Explorer: 
 Define Properties click this directly from the workflow tree to 
 proceed immediately to the selected step 
Visual MODFLOW Flex Exercise: Valley 
 
© Waterloo Hydrogeologic Page 10 
  Layer ensure the Layer view is active (Layer 1) 
  Wells add a check mark in the Model Explorer to make the 
 pumping wells visible 
  Constant Heads add a check mark in the Model Explorer to make the 
 constand head boundary conditions visible 
The 2D viewer should look like the image below, with three light brown pumping wells (pbore_1, 
pbore_2 and pbore_3) distributed in the middle area across the three property zones, another 
line of light brown pumping wells on the left border of the model, and a line of red cells indicating 
a constant head boundary on the right border of the model: 
 
In the Model Explorer, under the Wells node: 
 Right Click ‘Wells’ from the Model Explorer 
 Edit Boundary Condition from the menu that appears 
This will open the Edit Wells window. 
Visual MODFLOW Flex Exercise: Valley 
 
© Waterloo Hydrogeologic Page 11 
 
Click on each pumping well in succession and you can see that there are two distinct groups of 
pumping wells for this model. Note that pbore_1 through pbore_3 have negative pumping rates, 
and are used to simulate extraction wells. Well-1 to Well-22), which are located at the left-hand 
end of the model, have a positive pumping rate and are used to simulate a specified flow 
boundary. 
 OK 
A constant head boundary has been assigned to the right-hand side of the model. To review the 
properties associated with this boundary condition: 
 Right-click ‘Constant-Head(1)’ from the Model Explorer 
 Edit Boundary Condition… from the menu that appears 
This will open the Edit boundary condition window, as shown in the image below: 
Visual MODFLOW Flex Exercise: Valley 
 
© Waterloo Hydrogeologic Page 12 
 
 We see that a constant head of 50 m is applied to the eastern fixed-head cells of the domain for 
a time period of 0 to 91.3 days. In the absence of any additional input, the model assumes that 
the same boundary is applied for the duration of the simulation. 
 Cancel 
Recharge, which shows seasonal variation, will be applied as a transient boundary condition over 
four stress periods. Given the seasonally varying boundary conditions, the modelled year is 
divided into four stress periods of 15 time steps each. Each stress period is 91.3 days (totalling 
365.2 days in all), and the time step multiplier is 1.2. The recharge boundary condition has been 
applied to the entire top layer of the model. Activating this boundary condition by adding a ‘’ 
in the Model Explorer will simply show a white dot in every cell (try for yourself). This isn’t very 
informative, so let’s open the Edit boundary condition window to review this values: 
 Right-click ‘Constant-Head(1)’ from the Model Explorer 
 Edit Boundary Condition… from the menu that appears 
The following Edit boundary condition window will open: 
Visual MODFLOW Flex Exercise: Valley 
 
© Waterloo Hydrogeologic Page 13 
 
 
You can click through each of the four stress period specified on the left hand-side of the window 
to review the recharge rate in each stress period. 
 Cancel 
1.4 Review of ‘Observed’ values 
Now we’ll inspect the input values for our head observations. These are the values which PEST 
will use to try and calibrate the model. First we’ll activate the observation wells in the 2D viewer, 
then we’ll review the values in a spreadsheet: 
  Observations add a check mark in the Model Explorer 
  Heads Observations add a check mark in the Model Explorer to make the 
 observation wells visible 
The 2D viewer should look like the image below: 
Visual MODFLOW Flex Exercise: Valley 
 
© Waterloo Hydrogeologic Page 14 
 
Now we will review the actual observation data in an excel spreadsheet: 
 Right-click ‘Heads Observations’ from the Model Explorer, under Observations 
 Edit Attributes… from the menu that appears 
The following excel spreadsheet will open, as shown below: 
Visual MODFLOW Flex Exercise: Valley 
 
© Waterloo Hydrogeologic Page 15 
 
This window allows you to view the time-varying observed heads that will be used to calibrate 
the groundwater flow model. 
In most practical cases, borehole observation data are too numerous to type in by hand. These 
values were imported from an ASCII text file. The observation values are used by PEST to calibrate 
the model. 
 to close the Observation data excel sheet 
The “observed” values included in this model were generated by a previous simulation using a 
set of conductivity and storage values that are unknown to you. The following screen capture 
shows the water levels observed by this previous simulation at the four observation wells, using 
a simple Excel time-series chart. These are the “observed data” that will be used to calibrate the 
model. 
Visual MODFLOW Flex Exercise: Valley 
 
© Waterloo Hydrogeologic Page 16 
 
The objective of this exercise is for you to calibrate the model against the observed values. 
Initially you’ll try calibrating the model manually and subsequently using PEST. First, we’ll run the 
model to compare the calculated and observed values for the initial set of parameters. 
 
Visual MODFLOW Flex Exercise: Valley 
 
© Waterloo Hydrogeologic Page 17 
PART 2: RUNNING THE MODFLOW MODEL 
You are now ready to perform the groundwater flow and particle pathline simulation by running 
MODFLOW 2005 in transient mode. From the Numerical Modeling workflow: 
 Translate to proceed directly to the Translate workflow step 
In this window let’s make sure the selected Run Type is transient flow: 
 Settings under the MODFLOW-2005 node in the Settings tab 
 Transient from the dropdown menu under Run Type 
Verify that the model will run for four stress periods each of 91.3 days duration. You should see 
a table under the MODFLOW-2005/Settings node which lists four Stress Periods, with 10 time 
steps each, as shown below: 
 
Also ensure the WHS solver is selected: 
 Solvers under the MODFLOW-2005 node in the Settings tab 
 BiCGSTAB-P Matrix Solver (WHS) from the dropdown menu for Selected Solver 
 Type: 0.0001 under Head change criterion (HCLOSE) 
 Type: 0.0001 under Residual