Building Hydrogeological Models to Export to Modflow using Geomodelr.

Hydrogeological models help us to understand and manage groundwater resources. This post is a review of what we have done in our webinars about hydrogeological models and groundwater modeling.

Ricardo Serrano


As we are going to have a new webinar really soon, we figured some of you might want to review our tools to create hydrogeological models and export them to Modflow. We introduced those tools in previous webinars creating a 3D geological models and used it in Modflow to estimate groundwater flow. Our first hydrogeology webinar was about exporting a non-faulted model. The second was about exporting a faulted model. Our next webinar will be about FEFLOW, but we are still preparing the details so this review will come in handy. If you haven’t, Sign Up for Free to Geomodelr to receive an invitation.

Pathlines in Model Muse
Image of flow paths in model muse from the hydrogeological model generated in our first webinar.


Introduction to Geomodelr

What’s Geomodelr? Geomodelr is the first web geological modeling platform. With it you can create 3D geological models by interpreting all the information you have available. For example, you can use geological maps, structural data, boreholes, or geophysical images. Buildhing cross sections is the way interpretation is done in Geomodelr, the most natural way for a Geologist.

Geomodelr’s basic feature is that, even when you start creating your model, it’s solid: there’s one and only one unit in any given point in the space below the topography, and given a point at a cross section, the unit is equal to the unit at the point.

We believe at Geomodelr that all geological representations should be solid. Furthermore, we initially created Geomodelr for numerical problems and those problems need solid models. By comparison, most platforms just create surfaces that you stitch together until you have a solid.  

The algorithm was used to simulate an earthquake first. Such task required a distributed model that could be used in hundreds or thousands of computers. You can use Geomodelr right now to understand the geological settings of a region in 3D and generate volumes or surfaces with complex faulting and pinching. Also, the Hydrogeologist plan allows you to generate hydrogeological models for groundwater flow estimation and export them to MODFLOW and FEFLOW.

Block Diagram of the model generated in our first webinar. You can share interactive visualizations of a public study from Geomodelr in your website.

Hydrogeological Conceptual Models

To be able to understand and relate the hydrological inputs and outputs you need to relate the physical environment and hydroclimatology to the local and regional geological settings. This is called a hydrogeological conceptual model. There’s plenty of literature about hydrogeological conceptual models, which we will not review here, but usually the following are the components of a conceptual hydrogeological model.

Hydrogeological Conceptual Model Contents
Usual contents of hydrogeological models

Geomodelr is good at defining the geometry of the model. That might be the most time consuming task of creating a hydrogeological model. Furthermore, this task is usually done directly at the cell level in a preprocessor like Model Muse, which is suboptimal. Hydrogeologists are very limited with this method. There are alternatives that allow you to create hydrogeological models that are meshed afterwards, but they are very expensive. We are confident Geomodelr is the easiest, fastest and most affordable alternative in the market.

Geomodelr has the very interesting feature of joining geological units. You might create a lithology model or an stratigraphic model that way. Afterwards, you can join the units according to their hydrological properties to generate the hydrogeological model.

First Steps to Build your Model in Geomodelr

After giving a name and a short description to your geological study you can enter to the study page. In the study page you will find 3 tabs: the Geological Model, the Model Settings and the Study Settings. You can also view the files repository, where you can upload shapefiles, excel files, GeoTiffs and png or jpg images. Learn more about the study page, how to upload and files and georeference images in our tutorial:

You can check how to georeference a model in the following tutorial: Georeferencing your Geological Model. This task is probably the most tricky in Geomodelr, so don’t hesitate to ask anything to or to the chat.

A short description of what you should do to georeference a model is the following: 

  1. If you have a geological map and a topography, and they are correctly georeferenced, Geomodelr can calculate the coordinate system as either the one of the map and if there is no map but there’s a topography, the one of the topography.

  2. If the coordinate system selected is not local, (i.e. it’s in degrees like WGS84), you will have problems so please select a local (flat) coordinate system.

  3. The area modeled will be the intersection between uploaded map and uploaded topography.

  4. If you did not select a map, and did not select a topography you will have to enter the area manually.

  5. First you will have to pick a coordinate system in numeric EPSG format.

  6. Finally, you will need to select a bounding box by either clicking two corners in the map or entering the bounding box in the coodinate system manually.

  7. After clicking Create Model and waiting a few minutes everything will be set up for you.

Building Hydrogeological Models Ready to Export

Creating your first cross section gives you an extrapolated solid model, so you should do that now. This cross section is important, as it defines the direction of interpolation. To save time, it should be perpendicular to the most important structures, or you will have to create many more cross sections to get a good model. Click in New Cross Section and then new empty or interpolated cross section. Wait a few seconds and you will have your first cross section to digitize. Afterwards, you will see a small preview of the cross section and it will be transparent black, the color of the special NONE unit.

Enter to the cross section editor by clicking the newly created section. First, You will find the editor which has 3 kinds of operations: edit polygons, edit lines, and edit nodes. In this case, Polygons are geological units. Also, lines can be faults, veins or fractures. However, Only faults have power to modify the model. Node operations serve both line and polygon operations, to be able to divide polygons in other places, for example. If you want a full description of the editor operations and how to use each one, you can go to the following tutorials: and

The first cross section should be the one you take most care of. After you finish building your first cross section a solid model will be available for you to interpolate, so you can take advantage of it to build more cross sections until all your information and knowledge is reflected in your geological model.


To build a cross section that uses interpolation, click again in New Cross Section, new empty or interpolated cross section. If your first cross section was vertical, Geomodelr will force to draw a line parallel to the previous one, unless you want a cross section which is not part of the model interpolation. Click to interpolate the geology, and leave select automatically which cross sections to interpolate by default. After you do this, you will have a cross section that’s a copy of the first one, but with a new topography. It’s not very impressive yet, but it will save you a lot of time. If you want to check more about interpolation go to the following tutorials: After you have edited the first cross sections and used interpolation to create more cross sections faster, you will arrive to the point where your model will be ready to export.

To check your model you can go to the Visualizations Page. This page will have many ways to review your solid model in 3D. Among the possible visualizations, you will be able to build solids of your units, you can also build block diagrams with any shape you want. You can also build wireframes of faults, and plot boreholes. Finally you can combine everything into a single visualization to relate the different visualizations. You will see that the cross sections and visualizations should match almost perfectly. To view a full tutorial on visualizations go to:

Exporting to Modflow

Finally, to create the Modflow export, you should go to the exports page of your model and fill the information required. First write a name, and then for every unit check if the unit is active, fill horizontal hydraulic conductivity, horizontal anisotropy and vertical hydraulic conductivity. A rule of thumb hydrogeologists always use is to use 1/10th of the horizontal conductivity as vertical conductivity. 

If you did not simplify the units, you will see lots of units that are either unused, or could be grouped with other existing units. Go back to the study page and click the units manager. You can use the merge button to merge an unused unit to another, renaming that unit in all cross sections and saving you time during the export.

A new feature we introduced in our last webinar was to assign properties to faults. To enable it, click in Click to set hydraulic properties at faults. This will show you the different faults of the model. You don’t have to set data for all the faults, only the ones that you think should have special hydraulic properties. Also, you can select to enter regular properties or plane direction properties, which uses the dip and normal of the faults at every triangle to assign hydraulic properties.

Cells intersected with faults
Modflow visualizer that shows only the faults where hydraulic properties have been set for the hydrogeological model.

Meshing Algorithms

You have to enter the parameters of the finite differences mesh to finish the export. Currently, Geomodelr supports two meshing algorithms: simple and adaptive. For the simple algorithm you will have to enter the number of rows and columns and also the number of layers.

The adaptive algorithm tries to fit to the layers smoothly. To use it, you also need to enter the minimum thickness of the layer and control the maximum angle between two cells in a layer. This option is used to prevent very ugly geometries of the mesh. Also, the layers are initial, because they might be removed to simplify mesh.

After MODFLOW export is generated, it will appear in the right side of the exports page with the name of the export. If you download it it will have a .zip extension. If you want to change a parameter in the previous export, you can click the paste option in the export and the form will be filled with that data, and after you make the change you can create a new export.

You might have noticed that in the top of the exports page, there’s an option to export to FEFLOW®. Right now you can use the same meshing algorithms we used for MODFLOW® to export to FEFLOW®. It will generate a file with the units and all the information you need. However, we know that FEFLOW® supports other kinds of models, so don’t worry. You will soon will see what we have created in FEFLOW®. Sign up for FREE and you will receive an invitation to the webinar soon.

Origin of coordinates Geomodelr and Model Muse
The following image shows the place where the user must obtain the X and Y origin of coordinates plus where they should be put in Model Muse. Other preprocessors work the same.

Using the Model in Model Muse

Download the file to your PC and you will find .BAS, .DIS, .LPF and .NAM files. These files might be opened in any of the MODFLOW preprocessors that support MODFLOW 2005. Either Visual Modflow®, Model Muse®, or others.

Model Muse is free and was created by the USGS so that’s what we have used in our webinars. To use the exported file in Model Muse, extract them in a folder, open Model Muse, select Import MODFLOW 2005 Model. In the next screen select the origin of the model. The origin of the model can be seen in the Model Configuration tab of your Geomodelr study, as is shown below, just copy the left and lower values. After a few seconds, we can view the loaded objects. To view more about Model Muse usage, go to our previous webinars:

Hydrogeological models in FEFLOW
An image of an export to FEFLOW. We are working right now in better algorithms and we'll keep you updated about our next webinar.

Closing remarks

We hope you have enjoyed this review about the tools Geomodelr has to export hydrogeological models to MODFLOW. We are updating our algorithms all the time so you can have the best geological modeling platform possible and create the best geological or hydrogeological models. If you want to try the Hydrogeologist plan you can enjoy a FREE month. You will have a consultant teaching you the first steps in modeling, helping you be successful and generating the best hydrogeological models.

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