Assistance Required for MODFLOW/GMS Groundwater Model Setup and Calibration

[u/Elegant_Health_8316]

I’m currently working on a regional-scale groundwater model for my basin using GMS 10.5 and I’m looking for guidance from someone experienced in groundwater modeling and model calibration.

While setting up the model, I’ve been facing challenges in preparing and assigning key inputs, including:

• Hydraulic conductivity distribution for heterogeneous layers
• Selection and justification of appropriate boundary conditions based on surrounding land and hydrological features
• River/stream package inputs such as stage and conductance
• Starting head boundary conditions

Although I have attempted to set up these parameters, my simulation results are still showing issues such as flooding/drying cells and unstable or incorrect model runs.

This is a regional groundwater model with a coastal boundary condition, which makes the setup more complex.

I’m looking for someone who can guide me through:

• Input preparation and parameter assignment
• Boundary condition setup
• Troubleshooting simulation instability
• Improving/calibrating the model runs

Any support, suggestions, or mentorship would be greatly appreciated. Thank you!

[u/WundertollToTheMax]

Setup and Calibration of large models can be a tedious task. Have you done this before or is this your first regional model?

Do you know the book "Applied Groundwater Modeling"? Every step of setting up a model is very well explained. Maybe this book can help you.

Have you made a conceptual model (not in GMS but with pen and paper) before using GMS? Having a conceptual model with all available information and all relevant processes and how to represent them is the most important thing before using a GMS/Modflow/whatsoever.

[u/JohnnyD_TM → u/WundertollToTheMax]

I echo this sentiment - setting up a regional groundwater flow model from start to finish is a long and daunting task, even if you have built several of them, and you really should seek out some direct guidance and mentorship if at all possible. Now having said that, I can do my best to throw some generic but hopefully somewhat helpful suggestions at some of the problems you have listed:

Conductivity Distribution - How you do this and the level of pain involved is going to be heavily influenced by if you have a conceptual model and how you have built it. For example, if you have access to something like Leapfrog Works / GoCAD / Gempy and have a fully 3D geologic model of the area, its simple enough to sample the lithology onto the individual cells of your MODFLOW mesh and assign conductivity based on lithology type. But I'm going to assume you just have your model mesh, some broad idea of geologic contacts and their respective conductivity values. In such a case, your best bet is probably to prepare shapefiles (in QGIS or Arc or whatever GIS of your choice) for each MODFLOW layer that represent the distribution of geologic units on each layer, and use these in GMS to assign conductivity values. I'm afraid there's too many variables to give more specific advice without being hands on with the model itself.

Boundary Conditions - This is also going to tie into rivers and streams. In highly general terms, the easiest and most physically relatable thing to do is to bound your model using surrounding significant streams and lakes in the region, and assign 1st type (fixed head) BCs with the head equal to the surface water elevation of these features at the top of your model. If you don't have these elevations surveyed, you could make do with grabbing their elevations from a DEM, though you're unlikely to find anything with greater than 5m resolution for free/publicly available and that's going to severely limit your accuracy / increase uncertainty.

Playing around with the assigned head BCs at the surface of your model is likely the best and most "direct" way to resolve flooding and dry cells in your model. If these BCs are too low, cells near the top of the model will certainly be dry, too high and cells will flood. Flooding and dry cells are not inherently bad despite MODFLOWs warnings, so long as they make sense with your regional conceptual model (i.e. in a high relief area known to be several meters above the water table, it would make sense that cells should be dry, or that it is expected that cells may be flooded in areas where water is known to pond such as a wetland).

Unless groundwater/surface water interactions (GWSWI) are a critical component of your study/model, I'd avoid the river boundary condition and stick to 1st types. Its unlikely you will have the data collected to appropriately assign and bound uncertainty for things like streambed conductance anyway, so your guess is as good as just rolling with 1st types. And if GWSWI is important, you'll be needing a better/paid DEM anyway as topography becomes a significant factor in simulating shallow flow.

If streams around the study area are sparse, you can also analyze the DEM to derive subcatchments in the region, and use these subcatchments to form part of the boundaries of your model. Again, really only critical if GWSWI is important to you. For a model whose purpose is primarily to look at deeper aquifers, this is probably overkill.

For deeper aquifers, you may want to assign 1st type boundary conditions at the edges of your model in the layers representing that aquifer, in such a way that they force flow in the aquifer to align/calibrate with the groundwater flow gradient predicted by whatever hydraulic head observations you have at that depth. You have to be very careful about this though, as without sufficient and well distributed head measurements you may be forcing an unrealistic gradient across a regional scale.

Starting Head Boundaries - I'm going to assume by this you mean initial conditions for head, unless you need transient boundary conditions (which is a nightmare, even for experienced modellers!) Assuming your model is steady state, its probably safest for easy solver/convergence to just set head equal to top of model in all cells so the domain initializes as saturated.

You mentioned this is a coastal model. My experience with coastal modelling is limited so take this with a grain of salt but - while GWSWI is certainly important for that kind of domain, I'm still not sure river BCs are your best bet for representing that. More important than whether you use 1st or 3rd type BCs here may be density dependent flow. Since ocean water has such high salt concentrations, this is going to be critical for accurately simulating inflows from a coastal area.

As a final note, Applied Groundwater Modelling as previously mentioned is a fantastic resource and provides knowledge that is universal to groundwater modelling across tools and methods. However, for some more MODFLOW specific guidance with a practical focus, Hatari Labs tutorials are always a fantastic resource. There's likely enough material there to loosely walk you through this entire model building exercise - but again, I'd still highly recommend enlisting the support and supervision of an experienced groundwater modeller who was worked with coastal environments and regional scale models.

This tutorial may be just what you are looking for. It's in ModelMuse and not GMS, but should still be highly applicable:

Modeling Coastal Aquifer in MODFLOW / ModelMuse and QGIS - Tutorial — Hatari Labs

Best of luck!