Groundwater Modeling Software Distribution Sites:

USGS, Groundwater Modeling Software
EPA, Center for Subsurface Modeling Support
EPA, Software for Environmental Awareness
International Groundwater Modeling Center, School of Mines, Colorado
Scientific Software Group (commercial)
Rockware, Inc. (commercial)
Richard Winston's Groundwater Modeling Page
Hydrology, Hydraulics, Water Quality (HHWQ) modeling resources blog

Interactive Groundwater Modeling on the Web:

Interactive Groundwater Flow and Transport Models (Univ. of Illinois)

Groundwater Modeling Software (public domain/free of charge):

  MODFLOW 88/96/2000/2005 (USGS) - 3D finite difference, saturated flow
  SUTRA (USGS) - 2D/3D finite element, sat/unsat, variable density flow, transport, heat
  VS2DI (USGS) - 2D finite difference, unsat flow & transport, heat flow
  MT3DMS (University of Alabama) - 3D transport model to MODFLOW
  RT3D (Battelle Northwest Laboratory) - MT3DMS + multispecies reactions
  TOUGH2 (Lawrence Berkeley National Laboratory)- 3D multiphase/unsat flow & trans.
"Interactive Ground Water (IGW)" (Michigan State Univ.)  - integrated flow & transport
  ParFLOW (Lawrence Livermore National Laboratory) - 3D large grid flow
  ASMWin (ETH Zuerich) - 2D finite difference, flow and transport
  STOMP (Pacific Northwest National Laboratory) - 3D multiphase flow & transport
  IWFM (Ca. DWR) - 3D finite element groundwater & surface water flow model

GUIs for MODFLOW and other model codes (commercial):

  PMWIN (in the public domain)
  Groundwater Vistas
  Visual Modflow
  Argus ONE (generic GUI; specific interface to MODFLOW and other USGS software)
  Groundwater Modeling System (GMS)
  Petrasim (GUI for the TOUGH family of software, 3D modeling)

Groundwater Modeling Software (commercial):

  MODHMS (Hydrogeologic Inc) - MODFLOW based watershed model
  MODFLOW-SURFACT (Hydrogeologic Inc) - MODFLOW w/unsat/multiphase flow
  SWIFT (GeoTrans) - 3D finite difference, flow, heat, brine, & transport
  FEFlow (Wasy Ltd.) - 3D finite element flow & transport & watershed & heat
  IGSM (WRIME, Ca. Dept. Water Resources, U.S. Bureau of Reclamation)
  MikeSHE (DHI Water and Environment) - watershed model w/ MODFLOW

Groundwater Modeling Demonstrations and Reviews:

Flow and Transport Modeling, Homogeneous and Heterogeneous Aquifers (IGW)
Digital Library, Flow and Transport Modeling (IGW)
Groundwater Modeling Software Reviews (Int. Groundwater Modeling Center)
Boundary conditions - review for groundwater modelers (by E.P. Poeter, W.L. Wingle)

THE TEN COMMANDMENTS FOR GROUNDWATER MODELING (by Dawn H. Garcia)

Other Webpages with Modeling Links:

Online Site Assessment Tool (EPA) - web calculators, conversions & resources
Geochemical Modeling and Environmental Modeling Software Links
California Water and Environmental Modeling Forum
Vadose Zone Modeling Software Links (UC Davis Groundwater Coop. Ext. Program)