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ModelMuse: A Graphical User Interface for Groundwater Models

March 21, 2024

Overview of ModelMuse

Screenshot from ModelMuse.
Screenshot from ModelMuse showing example model parameters.

ModelMuse is a graphical user interface (GUI) for the U.S. Geological Survey (USGS) models MODFLOW 6, MODFLOW–2005, MODFLOW-LGR, MODFLOW-LGR2, MODFLOW-NWT, MODFLOW-CFP, MODFLOW-OWHM (versions 1 and 2), MODPATH, ZONEBUDGET, PHAST, SUTRA 2.2, SUTRA 3.0, SUTRA 4.0, MT3D-USGS, and WellFootprint and the non-USGS model MT3DMS. This software package provides a GUI for creating the flow and transport input file for PHAST and the input files for the other models. In ModelMuse, the spatial data for the model are independent of the grid, and the temporal data are independent of the stress periods. Being able to input these data independently allows the user to redefine the spatial and temporal discretization at will. ModelMuse supports parameter estimation with UCODE in MODFLOW–2005 and MODFLOW-NWT models and with PEST in MODFLOW and SUTRA models except for MODFLOW-LGR models.


Download Current Version of ModelMuse

The current release is ModelMuse v.

ModelMuse for Microsoft Windows Operating Systems

Users are encouraged to read the documents that are provided in the 'doc' directory of this software distribution, including the 'Release.chm' file. The recommended method of installing ModelMuse is with the installer. However, if there is difficulty in using the installer, ModelMuse can be installed by unzipping the zip file. The installer associates the extensions .gpt, .gpb and .mmZLib with ModelMuse. If the zip file is used instead of the installer, the user may wish to make those associations manually.


Documentation for ModelMuse

Version 2 Documentation:  Winston, R.B., 2009, ModelMuse-A graphical user interface for MODFLOW-2005 and PHAST: U.S. Geological Survey Techniques and Methods 6-A29, 52 p.

Version 3 Documentation:  Winston, R.B., 2014, Modifications made to ModelMuse to add support for the Saturated-Unsaturated Transport model (SUTRA): U.S. Geological Survey Techniques and Methods, book 6, chap. A49, 6 p.

Winston, R.B., and Goode, D.J., 2017, Visualization of groundwater withdrawals: U.S. Geological Survey Open-File Report 2017–1137, 8 p.

Version 4 Documentation: Winston, R.B., 2019, ModelMuse version 4—A graphical user interface for MODFLOW 6: U.S. Geological Survey Scientific Investigations Report 2019–5036, 10 p.,


How to Cite ModelMuse

This USGS software has two types of citations associated with it.

  1. The report citations are for the original reports or articles documenting the underlying theory, methods, instructions, and (or) applications at the time the initial version of the software was released. This digital object identifier (DOI) is for the report.
  2. The software release citation is for the software/code itself (now referred to by USGS as a "Software Release") and references a specific version of the code and associated release date. This DOI links to the code.

In instances where an author is citing use of this software, it would be appropriate to cite both the report documenting the code and the specific software release version that was used.

Report Citations for ModelMuse

Report citations for ModelMuse are provided above in the Documentation for ModelMuse section.

Software/Code Citation for ModelMuse version 5.2

Winston, R.B., 2024, ModelMuse version 5.2: U.S. Geological Survey Software Release, 21 March 2024,

Programs Related to ModelMuse


Find MODFLOW-Related Software

Visit the MODFLOW and Related Programs page for a list of MODFLOW-related software.


Example USGS Applications of ModelMuse

Abdelaziz, R., & Merkel, B. J. (2015). Sensitivity analysis of transport modeling in a fractured gneiss aquifer. Journal of African Earth Sciences, 103, 121-127.

Al-Maktoumi, Ali, El-Rawy, M., Zekri, S. Abdalla, O., 2015. "Managed Aquifer Recharge Using Treated Wastewater to Mitigate Seawater Intrusion Along Jamma Coastal Aquifer, Oman." Conference paper: 

Al-Maktoumi, A., El-Rawy, M. and Zekri, S. 2016. Management options for a multipurpose coastal aquifer in Oman. Arabian Journal of Geosciences (2016) 9: 636. doi:10.1007/s12517-016-2661-x

Antonellini, M., Cilona, A., Tondi, E., Zambrano, M., & Agosta, F. (2014). Fluid flow numerical experiments of faulted porous carbonates, northwest Sicily (Italy). Marine and Petroleum Geology, 55, 186-201.

Bloxom, L. F., & Burbey, T. J. (2015). Determination of the location of the groundwater divide and nature of groundwater flow paths within a region of active stream capture; the New River watershed, Virginia, USA. Environmental Earth Sciences, 74:2687-2699.

Burnette, M.C., Genereux, D.P., Birgand, F., In-situ falling-head test for hydraulic conductivity: evaluation in layered sediments of an analysis derived for homogenous sediments, Journal of Hydrology (2016), doi:

Chaussard, E., Bürgmann, R., Shirzaei, M., Fielding, E. J., & Baker, B. (2014). Predictability of hydraulic head changes and characterization of aquifer-system and fault properties from InSAR-derived ground deformation. Journal of Geophysical Research: Solid Earth, 119(8), 6572-6590.

Cox, Ryan William, 2013. "A model of contaminant transport, Saline Valley Aquifer, Gallatin County Illinois" Theses. Paper 1319. Southern Illinois University Carbondale.

Cravotta, C. A., Goode, D. J., Bartles, M. D., Risser, D. W., & Galeone, D. G. (2014). Surface water and groundwater interactions in an extensively mined watershed, upper Schuylkill River, Pennsylvania, USA. Hydrological Processes, 28(10), 3574-3601.

Ebrahim, G.Y., Villholth, K.G. & Boulos, M. Integrated hydrogeological modelling of hard-rock semi-arid terrain: supporting sustainable agricultural groundwater use in Hout catchment, Limpopo Province, South Africa. Hydrogeol J 27, 965–981 (2019).

El-Rawy, M., Zlotnik, V.A., Al-Raggad, M., Al-Maktoumi, A., Kacimov, A. and Abdalla, O., 2016. Conjunctive use of groundwater and surface water resources with aquifer recharge by treated wastewater: evaluation of management scenarios in the Zarqa River Basin, Jordan. Environmental Earth Sciences, 75(15), p.1146.

El-Rawy, M., et al., Hydrodynamics of porous formations: Simple indices for calibration and identification of spatio-temporal scales, Marine and Petroleum Geology (2016),

El-Zehairy, A. A., Lubczynski, M. W., Gurwin, J. 2017. Interactions of artificial lakes with groundwater applying an integrated MODFLOW solution, Hydrogeology Journal,

Grygoruk, M., Batelaan, O., Okruszko, T., Miroslaw-Swiatek, D., Chormanski, J., & Rycharski, M. (2011). Groundwater modelling and hydrological system analysis of wetlands in the Middle Biebrza Basin. In Modelling of hydrological processes in the Narew Catchment (pp. 89-109). Springer Berlin Heidelberg.

Grygoruk, M., Bankowska, A., Jablonska, E., Janauer, G. A., Kubrak, J., Miroslaw-Swiatek, D., & Kotowski, W. (2015). Assessing habitat exposure to eutrophication in restored wetlands: Model-supported ex-ante approach to rewetting drained mires. Journal of environmental management, 152, 230-240.

Hassan, S. T., Lubczynski, M. W., Niswonger, R. G., & Su, Z. (2014). Surface–groundwater interactions in hard rocks in Sardon Catchment of western Spain: An integrated modeling approach. Journal of Hydrology, 517, 390-410.

Hogeboom, H.J., 2013. On the influence of groundwater abstractions on Lake Naivasha’s water level. MSc Thesis, University of Twente, The Netherlands, 90 p.

Huang, X., Cao, G., Liu, J., Prommer, H., & Zheng, C. (2014). Reactive transport modeling of thorium in a cloud computing environment. Journal of Geochemical Exploration, 144, 63-73.

Khadim, F.K.; Dokou, Z.; Lazin, R.; Bagtzoglou, A.C.; Anagnostou, E. Groundwater Modeling to Assess Climate Change Impacts and Sustainability in the Tana Basin, Upper Blue Nile, Ethiopia. Sustainability 2023, 15, 6284.

Khan, M.R., Koneshloo, M., Knappett, P.S., Ahmed, K.M., Bostick, B.C., Mailloux, B.J., Mozumder, R.H., Zahid, A., Harvey, C.F., Van Geen, A. and Michael, H.A., 2016. Megacity pumping and preferential flow threaten groundwater quality. Nature communications, 7. doi: 10.1038/ncomms12833.

Khan, M. R., Michael, H. A., Nath, B., Huhmann, B. L., Harvey, C. F., Mukherjee, A., et al. (2019). High‐arsenic groundwater in the southwestern Bengal Basin caused by a lithologically controlled deep flow system. Geophysical Research Letters, 46. 

Kourakos, G., & Mantoglou, A. (2015). An efficient simulation-optimization coupling for management of coastal aquifers. Hydrogeology Journal, 23(6), 1167-1179.

Kruegler, James; Gomez-Velez, Jesus; Lautz, Laura K.; Endreny, Theodore A. 2020. "Dynamic Evapotranspiration Alters Hyporheic Flow and Residence Times in the Intrameander Zone." Water 12, no. 2: 424.

Kuniansky, E.L., 2016. Custom Map Projections for Regional Groundwater Models. Groundwater.

Larroque, F. and Franceschi, M. ( 2011). Impact of chemical clogging on de-watering well productivity: numerical assessment. Environmental Earth Sciences, 64: 119-131.

La Vigna, F., Demiray, Z., & Mazza, R. (2014). Exploring the use of alternative groundwater models to understand the hydrogeological flow processes in an alluvial context (Tiber River, Rome, Italy). Environmental Earth Sciences, 71(3), 1115-1121.

Lekula, Moiteela and Lubczynski, Maciek W. 2019. Use of remote sensing and long-term in-situ time-series data in an integrated hydrological model of the Central Kalahari Basin, Southern Africa, Hydrogeology Journal 27:1541–1562,

Maslia, M. L., Suárez-Soto, R. J., Sautner, J. B., Anderson, B. A., Jones, L. E., Faye, R. E., ... & Moore, S. M. (2013). Analyses and historical reconstruction of groundwater flow, contaminant fate and transport, and distribution of drinking water within the service areas of the Hadnot Point and Holcomb Boulevard water treatment plants and vicinities, US Marine Corps Base Camp Lejeune, North Carolina—Chapter A: Summary and findings. Atlanta, GA: Agency for Toxic Substances and Disease Registry.

Michael, H.A. and Khan, M.R., 2016. Impacts of physical and chemical aquifer heterogeneity on basin-scale solute transport: Vulnerability of deep groundwater to arsenic contamination in Bangladesh. Advances in Water Resources, 98, pp.147-158. doi: 10.1016/j.advwatres.2016.10.010

Mohammed, K., 2019, MODFLOW-Farm Process Modeling for Determining Effects of Agricultural Activities on Groundwater Levels and Groundwater Recharge, J. Soil Groundwater Environ. Vl. 24, No. 5, p. 17-30,


Morgan, Huw and Willgoose, Garry. Testing the suitability of modflow for interpreting pump tests in a hydraulically fractured well [online]. In: Hydrology and Water Resources Symposium 2012. Barton, ACT: Engineers Australia, 2012: 68-75.

Naranjo, R.C., Welborn, T.L., and Rosen, M.R ., 2013, The distribution and modeling of nitrate transport in the Carson Valley alluvial aquifer, Douglas County, Nevada: U.S. Geological Survey Scientific Investigations Report 2013–5136, 51 p.

Nyende, J., Van, T. G., & Vermeulen, D. (2013). Conceptual and Numerical Model Development for Groundwater Resources Management in a Regolith-Fractured-Basement Aquifer System. J Earth Sci Clim Change, 4(156), 2.

Rios, J.F., 2016. GIS-Based Model for Estimating Nitrate Fate and Transport from Septic Systems in Surficial Aquifers. MSc Thesis, The Florida State University, 140 p.

Singh, A., Bürger, C. M., & Cirpka, O. A. (2013). Optimized sustainable groundwater extraction management: general approach and application to the City of Lucknow, India. Water resources management, 27(12), 4349-4368.

Suárez-Soto RJ, Jones LE, and Maslia, ML. 2013. Simulation of Three-Dimensional Groundwater Flow—Supplement 4. In: Maslia ML, Suárez-Soto RJ, Sautner JB, Anderson BA, Jones LE, Faye RE, Aral MM, Guan J, Jang W, Telci IT, Grayman WM, Bove FJ, Ruckart PZ, and Moore SM. Analyses and Historical Reconstruction of Groundwater Flow, Contaminant Fate and Transport, and Distribution of Drinking Water Within the Service Areas of the Hadnot Point and Holcomb Boulevard Water Treatment Plants and Vicinities, U.S. Marine Corps Base Camp Lejeune, North Carolina—Chapter A: Summary and Findings. Atlanta, GA: Agency for Toxic Substances and Disease Registry.

Switzman, H., Coulibaly, P., & Adeel, Z. (2015). Modeling the impacts of dryland agricultural reclamation on groundwater resources in Northern Egypt using sparse data. Journal of Hydrology, 520, 420-438.

Tian, Y., Zheng, Y., Wu, B., Wu, X., Liu, J., & Zheng, C. (2015). Modeling surface water-groundwater interaction in arid and semi-arid regions with intensive agriculture. Environmental Modelling & Software, 63, 170-184.


Varghese, G. K., Alappat, B. J., and Samad, M. S. A., 2015. MT3DMS and genetic algorithm in environmental forensic investigations. Procedia Environmental Sciences 30, 85 - 90.


Misut, P.E., Casamassina, N.A., and Walter, D.A., 2021, Delineation of areas contributing groundwater and travel times to receiving waters in Kings, Queens, Nassau, and Suffolk Counties, New York: U.S. Geological Survey Scientific Investigations Report 2021–5047, 61 p.,

Publication Year 2024
Title ModelMuse: A Graphical User Interface for Groundwater Models
Product Type Software Release
Record Source USGS Digital Object Identifier Catalog