Groundwater Modeling using Visual MODFLOW

October 1, 2020

Introduction to Groundwater Modeling with Visual MODFLOW Flex

Groundwater models are computer models that provide a simplified representation of the processes that occur in the natural groundwater environment.

Groundwater Modeling Overview

A groundwater model can help you to make predictions about the behavior of the groundwater flow system:

  • For water supply, is there is enough water – for operations or consumption?
  • What is the potential impact of pumping on the natural environment (surrounding private/public wells, rivers, lakes, streams, and aquatic habitats)?
  • What will happen when groundwater is pumped or injected at specified wells?

From a water quality perspective, it is important to know if the quality of groundwater will be suitable for the intended purposes (drinking, irrigation, industrial use, etc.). It is important to identify and understand sources of contamination, whether these are real or potential, how to mitigate the impacts. Sources of contamination that threaten groundwater supplies include:

  • Chemical spills, Leaky Underground Storage Tanks (USTs)
  • Landfill infiltration
  • Salt water intrusion
  • Septic systems
  • Infiltration to the groundwater from pesticides, fertilizers, road salt, etc.

Without groundwater models, it would be impossible to evaluate all of the natural processes that impact a hydrogeologic design because of complexities in:

  • the physical processes that occur in the hydrogeologic environment,
  • the spatial distribution of properties and boundaries,
  • the temporal nature of the flow system

Once a groundwater model has been developed and calibrated, it can used it to evaluate/ask “what if” questions about how the hydrogeologic system responds to design changes in the future. For example, you can add a groundwater design (i.e. the addition of pumping wells and injection wells, infiltration galleries, grout cut-off walls, seepage drains, etc …) to the model to simulate their impact on the hydraulic heads and flow before they are ever constructed in the field, providing significant time and cost savings.

How is the groundwater system represented in a computer model?

A groundwater model can incorporate all of these complexities, and assess different options and future conditions. When you are developing a groundwater model, it is necessary to translate the physical world into the modeling program. Geology becomes the hydrogeologic parameters such as conductivity and storativity. Hydrologic boundaries that impact the groundwater flow system are known as boundary conditions in a model, and include areas of recharge, rivers, lakes, wells, etc.  In the physical world, you have field observations such as groundwater levels, fluxes, or contaminant concentrations, and these are used to calibrate the model, making the model most closely match to what is observed in the real world.

The better that you can represent the physical world in the groundwater model, the more reliable the predictions can be.

Groundwater models can be used to:

What types of groundwater models are available?

There are a variety of groundwater numerical computer models: Finite Difference, Finite Element, and Finite Volume.  More details on each of these can be found below:

MODFLOW is developed by the U.S. Geological Survey (USGS); it is a three-dimensional (3D) finite-difference groundwater model. MODFLOW is considered an international standard for simulating and predicting groundwater conditions and groundwater/surface-water interactions”. MODFLOW has been used for more than 30 years, and is widely accepted for its easy of use and flexibility in working with other programs. The code is developed in FORTRAN and runs in a DOS window taking a variety of text files as inputs, and generated both text and binary output files.

Since the first release of MODFLOW in the 1980’s, there have been numerous advancements to the MODFLOW code and its capabilities. The most widely used versions are below.

  • MODFLOW-2000
  • MODFLOW-2005
  • MODFLOW-SURFACT (A proprietary version developed by HydroGeoLogic, Inc (HGL)

Complimentary programs and utilities for MODFLOW

MODFLOW calculates hydraulic heads and Darcy velocity. Additional programs and utilities have been developed to work with the outputs from MODFLOW and “fill” additional gaps for a groundwater modeling project.  The most commonly used ones are listed below:


Sub-regional flow budgets are water budget analyses that are completed on a part of the study area to characterize the contribution of each component of the hydrologic cycle to the health of the system. They are performed as a part of:

  • sub-watershed analyses
  • investigations on pumping impacts on streamflow
  • determining flows across political boundaries
  • water rights appropriation
  • analyzing seepage discharge rates
  • determining contaminant loading to wells, streams, etc.

ZONEBUDGET is the numerical model that calculates sub-regional water budgets for user-defined “zones” in a MODFLOW simulation. A zone is simply a polygon of MODFLOW cells that are combined into a common block of cells. White is the default (Zone 1), blue (Zone 2), green (zone 3), …MODFLOW provides cell-by-cell flow terms in the *.FLO output file (binary format) ZoneBudget uses the flow terms in this file to tabulate the budget data for each zone.

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MODPATH is a particle-tracking post-processing package developed to compute 3-dimensional flow paths using output from steady-state/transient MODFLOW simulations. MODPATH helps to conceptualize and quantify the source areas for water entering the flow system, and the discharge areas for flow exiting the groundwater system (as well as all points in-between). MODPATH uses a semi-analytical particle tracking scheme that allows an analytical expression of the particle’s flow path to be obtained within each finite-difference grid cell based on the heads from the MODFLOW simulation, which are calculated numerically.

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MT3DMS is a modular 3-dimensional transport model that simulates 3D advective-dispersive transport of dissolved solutes in groundwater. It is linked to MODFLOW output through the use of the LMT package.  MT3D was developed by Chunmiao Zheng at S.S. Papadopulos (1990). MT3DMS can simulate reactive TRANSPORT of dissolved solutes in groundwater including the following common problems: dissolved plumes, simple reactive transport, injection wells, waste lagoon, landfills, contaminant spills, non-point source pollution. MT3D does not model NAPLs, NAPL movement, or complex geochemical reactions (this last condition can be accommodated by PHT3D, learn more below)

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RT3D is a program for simulating reactive multi-species mass transport in three-dimensional groundwater aquifers. RT3Dv1.0 was first developed by P.T. Clement in 1997 for the Battelle Memorial Institute, Pacific Northwest National Laboratory, and was subsequently released into the public domain and quickly became an accepted standard for reactive transport modeling. Unfortunately, the code was based on MT3Dv1.5 and did not include many of the new solver technology implemented in MT3DMS. As a result, the application of RT3D was always hampered by excessively slow run-times.

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PHT3D is a multi-component transport model for three-dimensional reactive transport in saturated porous media. It couples the two existing and widely used computer programs, the solute transport model MT3DMS (v5.1, Zheng and Wang, 1998) and the USGS geochemical code PHREEQC-2 (v2.9, Parkhurst and Appelo, 1999). The coupled model forms a powerful and comprehensive three-dimensional reactive multi-component transport model (Prommer et al., 2003), which can handle a broad range of equilibrium and kinetically controlled biogeochemical processes, including aqueous complexation, redox reactions, mineral precipitation/dissolution and ion exchange reactions.


PEST (Parameter ESTimation) “is the industry standard software package for parameter estimation and uncertainty analysis of complex environmental and other computer models.” PEST is more than just a program, but comes with an in-depth set of utility programs that allows the program to be used in conjunction with groundwater models such as MODFLOW.