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U.S. Department of Energy
Reactive Transport in 3-Dimensions

RT3D Publications

Key RT3D Publications

This section lists documents that explain details of RT3D.  This includes documents written by the RT3D Development Team as well as documents on MT3DMS and MODFLOW.  Publications are nominally listed in order of importance.  Several white papers on RT3D updates or functionality are not listed here, but are available from the Code Documentation page.


  • Clement, T.P. 1997 RT3D - A Modular Computer Code for Simulating Reactive Multi-Species Transport in 3-Dimensional Groundwater Aquifers PNNL-11720 Pacific Northwest National Laboratory, Richland, Washington PDF File
  • Clement, T.P.Y. SunB.S. HookerJ.N. Petersen 1998a Modeling Multispecies Reactive Transport in Ground Water Ground Water Monitoring & Remediation 18279-92  [Abstract] (Reprint available upon .)
  • Johnson, C.D.M.J. TruexT.P. Clement 2006 Natural and Enhanced Attenuation of Chlorinated Solvents Using RT3D PNNL-15937 Pacific Northwest National Laboratory, Richland, Washington PDF File
  • Johnson, C.D.M.J. Truex 2006a RT3D Reaction Modules for Natural and Enhanced Attenuation of Chloroethanes, Chloroethenes, Chloromethanes, and Daughter Products PNNL-15938 Pacific Northwest National Laboratory, Richland, Washington PDF File
  • Johnson, C.D.M.J. Truex 2006b rtFlux: RT3D Flux Plane Utility PNWD-3720 Battelle – Pacific Northwest Division, Richland, Washington PDF File
  • Johnson, C.D.J.R. Spencer 2003 Modifications to MODFLOW and RT3D for Modelling Cyclic Seasonal Variations in Groundwater Flow Proceedings of Modflow and More 2003: Understanding through Modelling (Volume II) E. Poeter, C. Zheng, M. Hill, and J. Doherty, eds International Ground Water Modelling Center, Colorado School of Mines, Golden, Colorado pp. 764-768


  • Zheng, C.P.P. Wang 1999 MT3DMS:  A Modular Three-Dimensional Multispecies Transport Model for Simulation of Advection, Dispersion, and Chemical Reactions of Contaminants in Groundwater Systems; Documentation and User's Guide SERDP-99-1 United States Army Corps of Engineers, Engineer Research and Development Center, Vicksburg, Mississippi PDF File Available
  • Zheng, C. 2006 MT3DMS v5.2: Supplemental User's Guide University of Alabama, Tuscaloosa, Alabama PDF File Available
  • Zheng, C.M.C. HillP.A. Hsieh 2001 Modflow-2000, the U.S. Geological Survey Modular Ground-Water Model – User Guide to the LMT6 Package, the Linkage with MT3DMS for Multi-Species Mass Transport Modeling Open File Report 01-82 U.S. Geological Survey, Reston, Virginia PDF File Available


  • Harbaugh, A.W.E.R. BantaM.C. HillM.G. McDonald 2000 MODFLOW-2000, the U.S. Geological Survey Modular Ground-Water Model – User Guide to Modularization Concepts and the Ground-Water Flow Process Open File Report 00-92 U.S. Geological Survey, Reston, Virginia PDF File Available
  • Harbaugh, A.W. 2005 MODFLOW-2005, The U.S. Geological Survey Modular Ground-Water Model – the Ground-Water Flow Process Techniques and Methods 6-A16 U.S. Geological Survey, Reston, Virginia PDF File Available


  • Clement, T.P.N.L. Jones 1998 RT3D Tutorials for GMS Users PNNL-11805 Pacific Northwest National Laboratory, Richland, Washington PDF File

Application of RT3D

These publications discuss application of RT3D to field and theoretical problems and may involve case studies, lab work, and/or development of RT3D reaction modules.  Includes articles by the RT3D Development Team and third parties (sorted by author).  This list is intended to be representative, but not exhaustive.  Note that articles by third parties may (usually unwittingly) misrepresent the nature or capabilities of RT3D (e.g., see public availability and Battelle Laboratories [sic]); contact us if something appears confusing.

  • Atteia, O.M. FranceschiA. Dupuy 2008 Validation of Reactive Model Assumptions with Isotope Data:  Application to the Dover Case Environ. Sci. Technol. 4293289-3295
  • Biteman, S.E.D.W. HyndmanM.S. PhanikumarG.S.Weissmann 2004 Integration of Sedimentologic and Hydrologic Properties for Improved Transport Simulations Aquifer Characterization J.S. Bridge and D.W. Hyndman eds SEPM Special Publication 80 Society for Sedimentary Geology (SEPM), Tulsa, Oklahoma pp. 3-13
  • Bolisetti, T.S. Reitsma 2003 Numerical Simulation of Chemical Grouting in Heterogeneous Porous Media Grouting and Ground Treatment L.F. Johnsen, D.A. Bruce, and M.J. Byle, eds ASCE Publications, Reston, Virginia pp. 1454-1465 doi:10.1061/40663(2003)123
  • Borden, R.C 2007 Concurrent Bioremediation of Perchlorate and 1,1,1-Trichloroethane in an Emulsified Oil Barrier J. Contam. Hydrol. 941-213-33
  • Cadotte M.L. DeschênesR. Samson 2007 Selection of a Remediation Scenario for a Diesel-Contaminated Site Using LCA Intnl. J. LCA 124239-251
  • Clayton, M.H.R.C. Borden 2009 Numerical Modeling of Emulsified Oil Distribution in Heterogeneous Aquifers Ground Water 472246-258
  • Clement, T.P.Y.SunB.S. HookerJ.N. Petersen 1997 Modeling Natural Attenuation of Contaminants in Saturated Groundwater In Situ and On-Site Bioremediation:  Volume 1 A. Leeson and B.C. Alleman, eds Battelle Press, Columbus, Ohio pp. 37-42 (Presented at the Fourth International In Situ and On-Site Bioremediation Symposium, New Orleans, Louisiana, April 28-May 1, 1997.)
  • Clement, T.P.Y. SunC. Zheng 1998b RT3D - A Modflow-Family Reactive Transport Simulator Proceedings of MODFLOW '98 International Conference, Volume 1 E.P. Poeter, C. Zheng, and M.C. Hill, eds International Ground Water Modeling Center, Colorado School of Mines, Golden, Colorado pp. 397-403
  • Clement, T.P.C.D. JohnsonY. SunG.M. KleckaC. Bartlett 1999a Modeling Natural Attenuation of Chlorinated Solvent Plumes at the Dover Air Force Base Site Natural Attenuation of Chlorinated Solvents, Petroleum Hydrocarbons, and Other Organic Compounds A. Leeson and B.C. Alleman, eds Battelle Press, Columbus, Ohio pp. 29-34 (Presented at the Fifth International In Situ and On-Site Bioremediation Symposium, San Diego, California, April 19-22, 1999.)
  • Clement, T.P.C.D. JohnsonY. SunG.M. KleckaC. Bartlett 2000 Natural Attenuation of Chlorinated Solvent Compounds:  Model Development and Field-Scale Application at the Dover Site J. Contam. Hydrol. 422-4113-140
  • Clement, T.P.T.R. GautamK.K. LeeM.J. TruexG.B. Davis 2004 Modeling of DNAPL-Dissolution, Rate-Limited Sorption and Biodegradation Reactions in Groundwater Systems Bioremediation J. 81-247-64
  • Coulibaly, K.M.C.M. LongR.C. Borden 2006 Transport of Edible Oil Emulsions in Clayey Sands:  One-Dimensional Column Results and Model Development J. Hydrologic Engrg. 113230-237
  • Davis, J.H. 2003 Fate and Transport Modeling of Selected Chlorinated Organic Compounds at Hangar 1000, U.S. Naval Air Station, Jacksonville, Florida Water Resources Investigations Report 03-4089 U.S. Geological Survey, Tallahassee, Florida
  • Di Molfetta, A.R. Sethi 2006 Clamshell Excavation of a Permeable Reactive Barrier Environ. Geol. 503361-369
  • Geistlinger, H.D. EisermannM. SchirmerU. MayerT.P. Clement 2003 Development of New Modeling Tools for Simulating and Designing Reactive Gas Walls Groundwater Quality Modeling and Management Under Uncertainty S. Mishra, ed ASCE Publications, Reston, Virginia pp. 192-203 doi:10.1061/40696(2003)18
  • Gödeke, S.H-H. RichnowH. WeißA. FischerC. VogtH. BorsdorfM. Schirmer 2006 Multi Tracer Test for the Implementation of Enhanced In-Situ Bioremediation at a BTEX-Contaminated Megasite J. Contam. Hydrol. 873-4211-236
  • Gomez, D.E.P.C. de BlancW.G. RixeyP.B. BedientP.J.J. Alvarez 2008 Modeling Benzene Plume Elongation Mechanisms Exerted by Ethanol Using RT3D with a General Substrate Interaction Module Water Resour. Res. 445W05405 doi:10.1029/2007WR006184
  • Huang, J.J.A. ChristM.N. Goltz 2008 An Assembly Model for Simulation of Large-Scale Ground Water Flow and Transport Ground Water 466882-892
  • Johnson, C.D.R.S. SkeenD.P. LeighT.P. ClementY. Sun 1998 Modeling Natural Attenuation of Chlorinated Ethenes Using the RT3D Code Proceedings of the Water Environment Federation 71st Annual Conference and Exposition, WEFTEC '98, Volume 3 Water Environment Federation, Alexandria, Virginia pp. 225-247
  • Khadam, I.M.J.J. Kaluarachchi 2003 Multi-criteria Decision Analysis with Probabilistic Risk Assessment for the Management of Contaminated Ground Water Environmental Impact Assessment Review 236683-721
  • Langenhoff, A.A.M.J.J.M. StapsC. PijlsA. AlphenaarG. ZwiepH.H.M. Rijnaarts 2002 Intrinsic and Stimulated In Situ Biodegradation of Hexachlorocyclohexane (HCH) Water, Air, and Soil Pollution: Focus 23171-181
  • Lee, M-S.K-K. LeeY. HyunT.P. ClementD. Hamilton 2006 Nitrogen Transformation and Transport Modeling in Groundwater Aquifers Ecolog. Model. 1921-2143-159
  • Li, L.C.H. BensonE.M. Lawson 2005 Impact of Mineral Fouling on Hydraulic Behavior of Permeable Reactive Barriers Ground Water 434582-596
  • Li, L.C.H. BensonE.M. Lawson 2006 Modeling Porosity Reductions Caused by Mineral Fouling in Continuous-Wall Permeable Reactive Barriers J. Contam. Hydrol. 831-289-121
  • Lim, M-S.I.W. YeoT.P. clementY RohK-K. Lee 2007 Mathematical Model for Predicting Microbial Reduction and Transport of Arsenic in Groundwater Systems Water Res. 41102079-2088
  • Ling, M.H.S. Rifai 2007 Modeling Natural Attenuation with Source Control at a Chlorinated Solvents Dry Cleaner Site Ground Water Monitor. Remed. 271108-121
  • Lu, G.T.P. ClementC. ZhengT.H. Wiedemeier 1999 Natural Attenuation of BTEX Compounds: Model Development and Field-Scale Application Ground Water 375707-717
  • Lu, G.C. ZhengA. Wolfsberg 2005 Effect of Uncertain Hydraulic Conductivity on the Simulated Fate and Transport of BTEX Compounds at a Field Site J. Environ. Engr. 1315767-776
  • Mailloux, M.B. TartakovskyD. MiletteS.R. GuiotA. PeisajovichL. OlivierC. BélangerM-J. Lorrain 2002 Evaluation of a Carbon-Source Stimulated Bioremediation Technology for the Remediation of a Nitrate-Contaminated Aquifer at an Airport Site Ground and Water:  Theory to Practice D. Stolle, A.R. Piggott and J.J. Crowder, eds Southern Ontario Section of the Canadian Geotechnical Society, Toronto, Ontario, Canada pp. 919-925 (Presented at the 55th Canadian Geotechnical and 3rd Joint IAH-CNC and CGS Groundwater Specialty Conferences, Niagara Falls, Ontario, October 20-23, 2002.)
  • Phanikumar, M.S.D.W. HyndmanD.C. WiggertM.J. DybasM.E. WittC.S. Criddle 2002a Simulation of Microbial Transport and Carbon Tetrachloride Biodegradation in Intermittently-Fed Aquifer Columns Water Resour. Res. 3841033 doi:10.1029/2001WR000289
  • Phanikumar, M.S.D.W. HyndmanC.S. Criddle 2002b Biocurtain Design Using Reactive Transport Models Ground Water Monitor. Remed. 223113-123
  • Phanikumar, M.S.D.W. HyndmanX. ZhaoM.J. Dybas 2005 A Three-Dimensional Model of Microbial Transport and Biodegradation at the Schoolcraft, Michigan, Site Water Resour. Res. 415W05011 doi:10.1029/2004WR003376
  • Reed, P.B. MinskerA.J. Valocchi 2000a Cost-effective Long-term Groundwater Monitoring Design Using a Genetic Algorithm and Global Mass Interpolation Water Resour. Res. 36123731-3741
  • Reed, P.B. MinskerD.E. Goldberg 2000b Designing a Competent Simple Genetic Algorithm for Search and Optimization Water Resour. Res. 36123757-3761
  • Rolle, M.T.P. ClementR. SethiA.D. Molfetta 2008 A Kinetic Approach for Simulating Redox-controlled Fringe and Core Biodegradation Processes in Groundwater:  Model Development and Application to a Landfill Site in Piedmont, Italy Hydrol. Proc. J. 22254905-4921
  • Sun, Y.J.N. PetersenT.P. ClementB.S. Hooker 1998 Effect of Reaction Kinetics on Predicted Concentration Profiles During Subsurface Bioremediation J. Contam. Hydrol. 313-4359-372
  • Sun, Y.J.N. PetersenJ. BearT.P. ClementB.S. Hooker 1999a Modeling Microbial Transport and Biodegradation in a Dual-Porosity System Transport in Porous Media 35149-65
  • Tartakovsky, B.D. MilletteS. DelisleS.R. Guiot 2002 Ethanol-Stimulated Bioremediation of Nitrate-Contaminated Ground Water Ground Water Monitor. Remed. 22178-87
  • Tenbus, F.J.W.B. Fleck 2001 Simulation of Ground-Water Flow and Transport of Chlorinated Hydrocarbons at Graces Quarters, Aberdeen Proving Ground, Maryland Water Resources Investigations Report 01-4106 U.S. Geological Survey, Baltimore, Maryland
  • Truex, M.J.C.D. JohnsonJ.R. SpencerT.P. ClementB.B. Looney 2007 A Deterministic Approach to Evaluate and Implement Monitored Natural Attenuation for Chlorinated Solvents Remediation J. 17423-40
  • Uçankuş, T.K. Ünlü 2008 The Effect of Aquifer Heterogeneity on Natural Attenuation Rate of BTEX Environ. Geol. 544759-776
  • Wethasinghe, CS.T.S. YuenJ.J. KaluarachchiR. Hughes 2006 Uncertainty in Biokinetic Parameters on Bioremediation:  Health Risks and Economic Implications Environ. Intnl. 323312-323
  • Wood, R.C.J. HuangM.N. Goltz 2006 Modeling Chlorinated Solvent Bioremediation Using Hydrogen Release Compound (HRC) Bioremediation J. 103129-141
  • Wriedt, GM. Rode 2006 Modelling Nitrate Transport and Turnover in a Lowland Catchment System J. Hydrol. 3281-2157-176
  • Yan, S.B. Minsker 2006 Optimal Groundwater Remediation Design Using an Adaptive Neural Network Genetic Algorithm Water Resour. Res. 425W05407 doi:10.1029/2005WR004303

Related Topics

These publications discuss topics related to RT3D or that are of potential interest to RT3D users.  RT3D is typically ancillary to the main topic in these publications.  The RT3D FAQ lists additional documents related to specific questions and may also be of interest to RT3D users (i.e., articles on topics such as determination of dispersivity values).  Sorted by author.

  • Clement, T.P. 1998 Remediation of Contaminated Ground Water - Lessons from U.S.A. J. Indian Water Works Association 4241-247
  • Clement, T.P. 2001 A Generalized Analytical Method for Solving Multi-Species Transport Equations Coupled with a First-Order Reaction Network Water Resour. Res. 371157-163
  • Clement, T.P.B.M. PeytonT.R. GinnR.S. Skeen 1999b Modeling Microbial Transport and Accumulation Processes in Saturated Porous Media: A Review Advances in Nuclear Science and Technology:  Volume 26 J. Lewins and M. Becker, eds Kluwer Academic/Plenum Publishers, New York pp. 59-78
  • Clement T.P.V. SrinivasanC.D. JohnsonM.J. Truex 2006 Development of a New Analytical Tool for Modeling the Fate and Transport of Chlorinated Solvent Species WSRC-STI-2006-00076 Savannah River National Laboratory, Washington Savannah River Company, Aiken, South Carolina
  • Davis, R.J.N.L. JonesT.P. Clement 1998 Efficient Tools for Building Multi-Component Transport Models Proceedings of MODFLOW '98 International Conference, Volume 1 E.P. Poeter, C. Zheng, and M.C. Hill, eds International Ground Water Modeling Center, Colorado School of Mines, Golden, Colorado pp. 195-202
  • Lu, X.Y. Sun 2008 A Solution of Transport in Porous Media with Equilibrium and Kinetic Reactions Transp. Porous Media 722199-206
  • Magar, V.S.H.D. StenselJ.A. PuhakkaJ.F. Ferguson 1999 Sequential Anaerobic Dechlorination of Pentachlorophenol:  Competitive Inhibition Effects and a Kinetic Model Environ. Sci. Technol. 33101604-1611
  • Matott, L.S.A.J. Rabideau 2008 Calibration of Subsurface Batch and Reactive-Transport Models Involving Complex Biogeochemical Processes Adv. Water Resour. 312269-286
  • Palanichamy, J.T. BeckerM. SpillerJ. KöngeterS. Mohan 2009 Multicomponent Reaction Modelling Using a Stochastic Algorithm Comput. Visual. Sci. 12251-61
  • Peyton, B.M.T.P ClementJ.P. Connolly 2000 Modeling of Natural Remediation:  Contaminant Fate and Transport Chapter 5 in  Natural Remediation of Environmental Contaminants M. Swindoll, R.G. Stahl, and S.J. Ells, eds Society for Environmental and Toxicology and Chemistry, Pensacola, Florida pp. 79-120
  • Phanikumar, M.S.J.T. McGuire 2004 A 3D Partial-Equilibrium Model to Simulate Coupled Hydrogeological, Microbiological, and Geochemical Processes in Subsurface Systems Geophys. Res. Letters 3111L11503 doi:10.1029/2004GL019468
  • Sun, Y.T.P. Clement 1999 A Decomposition Method for Solving Coupled Multi-Species Reactive Transport Problems Transport in Porous Media 373327-346
  • Sun, Y.J.N. PetersenT.P. ClementR.S. Skeen 1999b Development of Analytical Solutions for Multi-Species Transport with Serial and Parallel Reactions Water Resour. Res. 351185-190
  • Sun, Y.J.N. PetersenT.P. Clement 1999c Analytical Solutions for Multiple Species Reactive Transport in Multiple Dimensions J. Contam. Hydrol. 354429-440

Submit Your RT3D-Related Publications

If you have used RT3D for reactive transport modeling and have published an article on the work, send an e-mail to with details, so we can list it here.

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