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Online Guides to USGS Versions of MODFLOW and associated packages:



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Anderson, M. P. and Woessner, W.W., 1992. Applied Groundwater Modeling: Simulation of Flow and Advective Transport. Academic Press Inc. San Diego, CA. 381 pp.


Anderson, M. P., Woessner, W.W., and Hunt, R.J., 2015. Applied Groundwater Modeling: Simulation of Flow and Advective Transport. Second Edition. Academic Press Inc. San Diego, CA.381 pp.


Aster, R.C., Borchers, B., and Thurber, C.H., 2005. Parameter estimation and inverse problems. Amsterdam, Elsevier Academic Press, 301 p.


ASTM, 1996. ASTM Standards on Analysis of Hydrologic Parameters and Ground Water Modeling. Publication Code Number (PCN): 03-418096-38. West Conshohocken, PA. Ph: 610/8329585. 146 pp.


Bard, J., 1974. Nonlinear parameter estimation. Academic Press. NY. 341 pp.


Bear, J., 1979. Hydraulics of Groundwater. McGraw-Hill. New York, NY. 567 pp.


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Clement, T. P., 1997. RT3D v1.0: A Modular Computer code for Simulating Reactive Multi-species Transport in 3-Dimensional groundwater systems. Pacific Northwest National Laboratory, Rihland, WA 99352, USA, PNNL-SA-11720, Found on-line at


Clement, T.P, Peyton, B.M., Skeen, R.S., Jennings, D.A., Petersen, J.N., 1997. Microbial growth and transport in porous media under denitrification conditions: Experiment and simulations, Journal of Contaminant Hydrology, 24, 269-285.


Clement, T.P., Sun, Y., Hooker, B.S., Petersen, J.N., 1998. Modeling multi-species reactive transport in groundwater aquifers, Groundwater Monitoring & Remediation Journal, vol 18(2), spring issue, p. 79-92.


Clement, T. P., 2003. RT3D v2.5 Update Document, February 2003. Pacific Northwest National Laboratory, Rihland, WA 99352, USA, PNNL-SA-11720.


Cosby, B.J., Hornberger, G.M., Clapp, R.B., and Ginn, T.R., 1984. A Statistical exploration of the relationship of soil moisture characteristics to the physical properties of soils, Water Resources Research 20(6): 682-690, 1984.


Cooley, R. L., 1983. Some new procedures for numerical solution of variably saturated flow problems. Water Resources Research, v19, no. 5. p. 1271-1285.


Demmel, J.W., 1997. Applied Numerical linear algebra: Philadelphia, Society for Industrial and Applied Mathematics, 419 p.


Doherty, J., 1998. Visual PEST: Graphical Model Independent Parameter Estimation. Watermark Computing and Waterloo Hydrogeologic Inc.


Doherty, J., 2003, Ground water model calibration using pilot points and regularization: Ground Water, v. 41, no. 2, p. 170–177.


Doherty, J., 2008, Using Pilot Points to Calibrate a MODFLOW/MT3D Model. Watermark Numerical Computing, Unpublished Training Workshop Material.


Doherty, J., 2015. Calibration and Uncertainty Analysis for Complex Environmental Models. Watermark Numerical Computing, Brisbane, Australia. ISBN: 978-0-9943786-0-6.


Doherty, J., 2021. PEST_HP: PEST for Highly Parallelized Computing Environments, Watermark Numerical Computing, October 2021.


Doherty, J., 2023a. PEST Model-Independent Parameter Estimation - User Manual Parts I and II, Watermark Numerical Computing, 7th Edition, January 2023 Revision.


Doherty, J., 2023b. PLPROC: A Parameter List Processor, Watermark Numerical Computing and Groundwater Model Decisions Support Initiative, April 2023.


Doherty, J. and Hunt, R, 2010. Approaches to highly parameterized inversion—A guide to using PEST for groundwater-model calibration: U.S. Geological Survey Scientific Investigations Report 2010–5169, 59 p


Domenico, P.A., and Schwartz, F. W., 1990. Physical and Chemical Hydrogeology. John Wiley and Sons Inc. New York, NY. 824 pp.


Driscoll, F.G., 1986. Groundwater and Wells, 2nd Edition. Johnson Division. St. Paul, Minnesota. 1089 pp.


Deutsch, C.V. and Journel, A.G., 1998. GSLIB Geostatistical Software Library and User’s Guide. Oxford University Press. N.Y. 369 pp.


Fetter, C.W., 1993. Contaminant Hydrogeology, Macmillan Publishing Co. New York, NY. 458 pp.


Fetter, C.W., 1994. Applied Hydrogeology, 3rd Edition. Macmillan Publishing Co. New York, NY. 691 pp.


Fetter, C.W., 1999. Contaminant Hydrogeology, 2nd Edition. Prentice-Hall Inc., New Jersey 500 pp.


Freeze, R.A., and Cherry, J.A., 1979. Groundwater. Prentice-Hall Inc. Englewood Cliffs, New Jersey. 604 pp.


Glover, F., 1986. Future paths for integer programming and links to artificial intelligence. Comp. and Operations Res., 5, p. 533-549.


Glover, F., 1989: Tabu Search - Part I, ORSA. J. Comp. 1(3), 190-206.


Goode, D.J., 1996, Direct simulation of groundwater age: Water Resources Research, v. 32, no. 2, p. 289–296.


Graham, D.N., Chmakov S., Sapozhnikov, A., and Gregersen, J.B., 2006. OpenMI Coupling of MODFLOW and MIKE 11. “MODFLOW and More 2006. Managing Ground Water Systems. Conference Proceedings” May 21-24, v2, p727-731.


Guo, Weixing, and Langevin, C.D., 2002. User's Guide to SEAWAT: A Computer Program for Simulation of Three-Dimensional Variable-Density Ground-Water Flow: Techniques of Water-Resources Investigations Book 6, Chapter A7, 77 p.


Guo, Zhaoli, and Zhao, T.S., 2005, Lattice Boltzmann simulation of natural convection with temperature-dependent viscosity in a porous cavity: Progress in Computational Fluid Dynamics v. 5, nos. 1/2, p. 110-117.


Halford, K.J. and Hanson R.T., 2002, User Guide for the Drawdown-Limited, Multi-Node Well (MNW) Package for the U.S. Geological Survey’s Modular Three-Dimensional Finite-Difference Ground-Water Flow Model, Versions MODFLOW-96 and MODFLOW-2000t: U.S. Geological Survey Open-File Report 02-293, 33 p.


Harbaugh, A.W. 1990. A computer program for calculating subregional water budgets using results from the USGS Modular Three-Dimensional finite-difference groundwater flow model. U.S. Geological Survey Open-File Report 90-392.


Harbaugh, A.W. 2005. MODFLOW-2005, The U.S. Geological Survey Modular Ground-Water Model—the Ground-Water Flow Process: U.S. Geological Survey Techniques and Methods Book 6, Chapter A16, 253 p.


Henry, R.M., 1995. A Critical Comparison of Some Commonly Used Groundwater Modeling Codes, M.Sc. Thesis. University of Waterloo, Department of Earth Sciences. Waterloo, Ontario. 115 pp.


Hill, M. C., 1990. Solving groundwater flow problems by conjugate-gradient methods and the strongly implicit procedure, Water Resources Research, 26(9), 1961-1969.


Hill, M. C., 1992. A Computer Program (MODFLOWP) for Estimating Parameters of a Transient, Three-Dimensional, Ground-Water Flow Model using Nonlinear Regression. U. S. Geological Survey Open-File Report 91-484.


Hill, M. C., 1997. Preconditioned Conjugate-Gradient 2 (PCG2), A Computer Program for Solving Groundwater Flow equations. USGS Water-Resources Investigations Report 90-4048.


Hughes, J.D., Langevin, C.D., and Banta, E.R., 2017, Documentation for the MODFLOW 6 framework: U.S. Geological Survey Techniques and Methods, book 6, chap. A57, 42 p.,


Hornberger, G.M., Mills, A.L., and Herman, J.S., 1992. Bacterial transport in porous media: Evaluation of a model using laboratory observations, Water Resources Research, 28(3), 915-938.


Huyakorn, P.S. and Pinder, G.F., 1983. Computational Methods in Subsurface Flow. Academic Press. New York, NY. 473 pp.


HydroGeoLogic, Inc., 1996. MODFLOW-SURFACT ver. 2.2 User’s manual. A three dimensional fully integrated finite difference code for simulating Fluid flow and Transport of contaminant in saturated-unsaturated porous media. Herndon, VA 20170, USA.


HydroGeoLogic, Inc., 2008. MOD-HMS/MODFLOW-SURFACT ver. 4.0 User’s manual. A Comprehensive MODFLOW-Based Hydrologic Modeling System. Herndon, VA 20170, USA.


Ibaraki, M., 2005, χMD User’s guide - An efficient sparse matrix solver library, Version 1.30. Columbus, Ohio State University School of Earth Sciences.


Kladias, M. P., and Ruskauff, G. J., 1997. Implementing Spatially Variable Anisotropy in MODFLOW. Ground Water, v35, no.2. p. 368-370


Koch, K., 1988. Parameter Estimation and Hypothesis Testing in Linear Models. Springer-Verlag, Berlin. 377 pp.


Konikow, L.F., Hornberger, G.Z., Halford, K.J., and Hanson, R.T., 2009. Revised multi-node well (MNW2) package for MODFLOW ground-water flow model: U.S. Geological Survey Techniques and Methods 6–A30, 67 p.


Langevin, C.D., Shoemaker, W.B., and Guo, Weixing, 2003. MODFLOW-2000, the U.S. Geological Survey Modular Ground-Water Model–Documentation of the SEAWAT-2000 Version with the Variable-Density Flow Process (VDF) and the Integrated MT3DMS Transport Process (IMT): U.S. Geological Survey Open-File Report 03-426, 43 p.


Langevin, C.D., Thorne, D.T., Jr., Dausman, A.M., Sukop, M.C., and Guo, Weixing, 2007. SEAWAT Version 4: A Computer Program for Simulation of Multi-Species Solute and Heat Transport: U.S. Geological Survey Techniques and Methods Book 6, Chapter A22, 39 p.


Langevin, C.D., Hughes, J.D., Banta, E.R., Niswonger, R.G., Panday, Sorab, and Provost, A.M., 2017, Documentation for the MODFLOW 6 Groundwater Flow Model: U.S. Geological Survey Techniques and Methods, book 6, chap. A55, 197 p.,


Langevin, C.D., Provost, A.M., Panday, S., and Hughes, J.D., 2022. Documentation for the MODFLOW 6 Groundwater Transport Model: U.S. Geological Survey Techniques and Methods, book 6, chap. A61, 56 p.,


Leake, S.A. and Lilly, M.R., 1997. Documentation of a Computer Program (FHB1) for Assignment of Transient Specified-Flow and Specified-Head Boundaries in Applications of the Modular Finite-Difference Ground-Water Flow Model (MODFLOW). U.S. Geological Survey Open-File Report 97-571.


Leonard, B.P., 1988. Universal Limiter for Transient Interpolation Modeling of the Advective Transport Equations: The ULTIMATE Conservative Difference Scheme. NASA Technical Memorandum 100916 (ICOMP-88-11). Institute for Computational Mechanics in Propulsion. Lewis Research Center, Cleveland Ohio.


Levenberg, K., 1944. A method for the solution of certain non-linear problems in least squares. Q. Appl. Math., v2. 164-168 pp.


MacDonald, M. G. and Harbaugh, A. W., 1988. MODFLOW, A Modular three dimensional finite- difference groundwater flow model: U. S. Geological Survey Techniques of Water-Resources Investigations, Book 6, Chapter A1, 586 pp.


MacDonald, M.G. and A.W. Harbaugh. 1996. User’s Documentation: MODFLOW-96, An update to the USGS Modular three-dimensional finite–difference groundwater flow model. U.S. Geological Survey Open File Report 96-485.


Markstrom, S.L., Niswonger, R.G., Regan, R.S., Prudic, D.E., and Barlow, P.M., 2008. GSFLOW—Coupled ground-water and surface-water flow model based on the integration of the Precipitation-Runoff Modeling System (PRMS) and the Modular Ground-Water Flow Model (MODFLOW-2005): U.S. Geological Survey Techniques and Methods 6-D1, 240 p.


Marquardt, D. W., 1963. An algorithm for least-squares estimation of nonlinear parameters. Journal of the Society of Industrial and Applied Mathematics, v11, no. 2. 431-441 pp.


Mehl, S.W., and Hill, M.C., 2001. MODFLOW-2000, The U.S. Geological Survey Modular Ground-Water Model - User Guide To The Link-AMG (LMG) Package For Solving Matrix Equations Using An Algebraic Multigrid Solver. U.S. Geological Survey Open-File Report 01-177.


Mehl, S.W. and Hill, M.C., 2005. MODFLOW-2005, the U.S. Geological Survey modular ground-water model -- documentation of shared node local grid refinement (LGR) and the Boundary Flow and Head (BFH) Package. U.S. Geological Survey Techniques and Methods 6-A12, 68 p.


Mehl, S.W., and Hill, M.C., 2013. MODFLOW-LGR -- Documentation of ghost node local grid refinement (LGR2) for multiple areas and the boundary flow and head (BFH2) package. U.S. Geological Survey Techniques and Methods 6-A44, 43 p.


Merritt, M., L. and Konikow, L. F., 2000. Documentation of a Computer Program to Simulate Lake-Aquifer Interaction Using the MODFLOW Ground-Water Flow Model and the MOC3D Solute-Transport Model. U.S. Geological Survey Water Resources Investigations Report 00-4167.


Mikhail, E. M., 1976. Observations and Least Squares. IEP. NY. 497 pp.


Muffels, C., Tonkin, M., Ramadhan, M., Wang, X., Neville, C., and Craig, J.R., 2016. User's Guide for mod-PATH3DU - A groundwater path and travel-time simulator. S.S. Papadopulos & Associates, Inc., Bethesda, MD. Version 1.1.0 September 2016.


Nash, J. C. and Walker-Smith, M., 1987. Nonlinear Parameter Estimation; an Integrated System in Basic. Marcel Dekker Inc. Monticello, NY. 493 pp.


National Ground Water Association, 1985, 1987, 1989, 1992... Practical Applications of Groundwater Models. Proceedings published by NGWA. Dublin, OH.


Nielsen, D.M. (editor), 1991. Practical Handbook of Ground Water Monitoring. Lewis Publishers. Chelsea, MI. 717 pp.


Niswonger, R.G. and Prudic, D.E., 2005. Documentation of the Streamflow-Routing (SFR2) Package to include unsaturated flow beneath streams - A modification to SFR1: U.S. Geological Survey Techniques and Methods, Book 6, Chap. A13, 47 p.


Niswonger, R.G., Prudic, D.E., and Regan, R.S., 2006. Documentation of the Unsaturated-Zone Flow (UZF1) Package for modeling unsaturated flow between the land surface and the water table with MODFLOW-2005. U.S. Geological Survey Techniques and Methods 6-A19, 62 p.


Ozbilgin, M.M. and Dickerman, D.C., 1984. A Modification of the Finite Difference Model for Simulation of a Two-Dimensional Ground-Water Flow to Include Surface-Ground Water Relationships: U.S. Geological Survey Water-Resources Investigations Report 83-4251, 98 pp.


Panday, S., Langevin, C.D., Niswonger, R.G, Ibaraki, M., Hughes, J.D., 2013. MODFLOW–USG Version 1: An Unstructured Grid Version of MODFLOW for Simulating Groundwater Flow and Tightly Coupled Processes Using a Control Volume Finite-Difference Formulation. U.S. Geological Survey, Chapter 45 of Section A, Groundwater Book 6, Modeling Techniques.


Pawlowski, J., 1991, Veranderliche stoffgroben in der ahnlichkeitstheorie, salle+sauerlander: Frankfurt, 108 p.


Peaceman, D.W., 1983. Interpretation of Well-Block Pressures in Numerical Reservoir Simulation with Nonsquare Grid Blocks and Anisotropic Permeability. Society of Petroleum Engineers Journal, v. 23, no. 3. p. 531-543


Poeter, E., Zheng, C., and Hill, M., (editors) 1998: MODFLOW’98. Colorado School of Mines. Golden, Colorado.


Pollock, D.W., 1994. User’s Guide for MODPATH/MODPATH-PLOT version 3: A particle tracking post-processing package for MODFLOW, the USGS finite-difference groundwater flow model. U.S. Geological Survey Open-File Report 94-464.


Pollock, David W., 1998. MODPATH, Documentation of Computer Programs to compute and display pathlines using results from U.S. Geological Survey modular three-dimensional finite difference groundwater flow model, U. S. Geological Survey Open Report 89-381, 188 pp.


Prommer, H., Barry, D.A., and C. Zheng, C., 2003. PHT3D - A MODFLOW/MT3DMS based reactive multi-component transport model. GroundWater, 42(2), 247-257.


Prudic, D.E., 1989. Documentation of a Computer Program to Simulate Stream-Aquifer Relations using a Modular, Finite-Difference, Ground-Water Flow Model. U. S. Geological Survey, Open-file report 88-729, 113 pp.


Prudic, D.E., Konikow, L.F., and Banta, E.R., 2004. A new stream-flow routing (SFR1) package to simulate stream-aquifer interaction with MODFLOW-2000: U.S. Geological Survey Open-File Report 2004-1042, 95 pp. (


Rhamadhan, M., 2015, A Semi-Analytical Particle Tracking Algorithm for Arbitrary Unstructured Grids. MASc. Thesis. University of Waterloo, Waterloo Ontario. (


Reddy, H.L., and Ford, R.M., 1996. Analysis of biodegration and bacterial transport: Comparison of models with kinetic and equilibrium bacterial adsorption, Journal of Contaminant Hydrology, 22, 271-287.


Shewchuck, J. R., 1970. Triangle: Engineering a 2D Quality Mesh Generator and Delaunay Triangulator.  School of Computer Science, Carnegie Mellon University, Pittsburg, PA. 10 pp.


Taylor, S.W., and P. R., Jaffe, 1990. Substrate and biomass transport in a porous medium, Water Resources Research, 26, 2153-2159.


United States Geological Survey, 2022. MODFLOW-6 - Description of Input and Output (Version 6.4.1). United States Geological Survey, Water and Science Availability and Use Science Program, MODFLOW 6 Development Team. Dec 2022.


van Genuchten, M.Th., 1980. A closed-form equation for predicting the hydraulic conductivity of unsaturated soils. Soil Science Society of America Journal. 44 (5): 892–898.


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Voss, C.I., 1984, A finite-element simulation model for saturated-unsaturated, fluid-density-dependent ground-water flow with energy transport or chemically-reactive single-species solute transport: U.S. Geological Survey Water-Resources Investigations Report 84-4369, 409 p.


Watson, D.F., 1994. Nngridr: an implementation of natural neighbor interpolation. 170 pp. Claremont, Australia.


White, J.T., and Hughes, J.D., 2011, An unstructured GPGPU preconditioned conjugate gradient solver for MODFLOW 2005, MODFLOW and More 2011, June 5–8, 2011, Golden, Colorado.


Zheng, C., 1993. Extension of the Method of Characteristics for Simulation of Solute Transport in Three Dimensions. Ground Water, vol 31(3). 456-465 pp.


Zheng, C., and Bennett, G. D., 1995. Applied Contaminant Transport Modeling: Theory and Practice, Van Nostrand Reinhold, New York.


Zheng, C., and Wang, P., 1999. MT3DMS, A Modular Three-Dimensional Multi-species Transport Model for Simulation of Advection, Dispersion, and Chemical Reactions of Contaminants in Groundwater Systems: Documentation and User’s Guide. U. S. Army Corps of Engineers, U. S. Army Engineer Research and Development Center, Vicksburg, Mississippi, SERDP-99-1.


Zheng, C. and Wang, P., 2003. MGO Modular Groundwater Optimizer Incorporating MODFLOW/MT3DMS: Documentation and User’s Guide. The University of Alabama, in cooperation with Groundwater Systems Research Ltd.


Zheng, C., 1999: User’s Guide. MT3D99 A modular 3D Multi-species transport simulator. S.S. Papadopulos & Associates.


Zysset, A., Stauffer, F., and Dracos, T., 1994. Modeling of reactive groundwater transport governed by biodegradation, Water Resources Research, 30(8), 2423-2434.



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