The program includes proprietary extensions, such as MODFLOW-SURFACT, MT3DMS (mass-transport 3D multi-species) and a three-dimensional model explorer.

The software is used primarily by hydrogeologists to simulate groundwater flow and contaminant transport.

The original version of Visual MODFLOW, developed for DOS by Nilson Guiguer, Thomas Franz and Bob Cleary, was released in August 1994.

A .NET version that included non-grid-based, graphical conceptual modelling features was released in 2012.

On January 10, 2005, Waterloo Hydrogeologic was acquired by Schlumberger's Water Services Technology Group.