An Introduction to Groundwater Modeling Concepts

Groundwater models are computer models that provide a simplified representation of the processes that occur in the natural groundwater environment. Models are tools used by hydrogeologists to simulate and predict aquifer conditions. The following topics will be covered:

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. Learn more

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)

Learn more about the history of MODFLOW, and what version is recommended based on your modeling objectives

Complementary 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.

What is Visual MODFLOW (Flex and Classic)

The input files that USGS MODFLOW requires to run a groundwater flow simulation are a series of text files, which describe all of the attributes of the model domain including cell-by-cell dimensions, properties and boundaries. MODFLOW reads these text files and uses them to calculate the hydraulic head in every active finite-difference grid cell. The fact that these input files are text files makes it difficult and time consuming to use the USGS MODFLOW directly to create a groundwater model. This has led to the development of Graphical User Interfaces (GUIs), including Visual MODFLOW (VMOD), that allow you to develop groundwater models graphically on-screen, using data files/sets that are common to a hydrogeologist, such as Excel and Databases, Surfer Grids, AutoCAD and GIS data (shapefiles, etc.).  Using Visual MODFLOW, you import your data sets and assign the cell dimensions, property values and boundary conditions graphically in row, column and layer view and then translate this Visual MODFLOW information into the set of MODFLOW input text files that are run by USGS MODFLOW to generate a groundwater flow solution. The Visual MODFLOW GUI also assists with the post-processing: interpreting the raw text and binary output files generated by MODFLOW and producing easy-to-understand color/contour maps and charts in order to assist with the analysis and interpretation of the model results.


The Visual MODFLOW GUI also works with other “add-ons” FORTRAN programs (the accessory programs mentioned above) for MODFLOW, by easing the generation of the input files and analyzing the results.

What is Visual MODFLOW Classic?

The first version of Visual MODFLOW “Classic” was released in 1994, and utilizes a strictly “numerical approach” to groundwater modeling (designing a MODFLOW grid and assigning model parameters to that grid). Over the years, this approach lead to several frustrations for modelers as it limited the ability to change/refine the numerical model grid as the modeling objectives changed, often requiring hours of manual, tedious work and iterative model development. Due to the design, the Visual MODFLOW (VMOD) Classic GUI also only works with regular versions of MODFLOW; the more enhanced versions that included Local Grid Refinement (LGR) and UnStructured Grids (USG) are not supported.

What is Visual MODFLOW Flex?

The Visual MODFLOW “Flex” GUI introduced the concept of a Conceptual Modeling approach, which dramatically improves the modeling experience by providing more flexibility to adapt numerical models as the objectives change.  The inputs for the groundwater model are designed in a conceptual model, using a variety of 2D and 3D shapes, with attributes.  Since the conceptual model objects are not assigned to a particular numerical model grid (or scheme), this makes is a breeze to change the numerical model as needed.  The VMOD Flex GUI also provides a similar set of numerical modeling capabilities as available in VMOD Classic.

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What are the differences between VMOD Flex and VMOD Classic

When you purchase a Visual MODFLOW license, you get access to the Visual MODFLOW “Classic” program and the Visual MODFLOW “Flex” program; there are some numerical modeling aspects that are not yet supported in VMOD Flex, mainly the SEAWAT and RT3D programs, and the Streams boundary condition.

Further Reading:


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See examples of how Visual MODFLOW has been used to:

Getting Started

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Visual MODFLOW Users Group on LinkedIn

Join the growing online community of Visual MODFLOW users on the LinkedIn Visual MODFLOW Users Group. Now with over 1500 members, it is one of the biggest online groundwater modeling groups on the web. Membership is free and only requires a free LinkedIn account.

Visit the Visual MODFLOW Users LinkedIn Group