It depends upon the purpose ...

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It depends upon the purpose of study and available data. A number of software for groundwater flow, transport, and geochemical reactions, including groundwater/surface-water interactions; variably-saturated flow and transport; hydrograph-separation and other streamflow-based programs; analysis of aquifer tests and slug tests; graphical user interfaces and post processors are available at USGS website http://water.usgs.gov/software/lists/groundwater/ . MODFLOW is the most widely used Modular Three-Dimensional Groundwater Flow Model.