MapWindow GIS and its associated MapWinGIS ActiveX Control were originally developed by Daniel P. Ames and a team of professors and students at Utah State University in 2002-2003 as part of a research project with the Idaho National Laboratory in Idaho Falls, Idaho as a GIS mapping framework for watershed modelling tools in conjunction with source water assessments conducted by the laboratory.

[2] In 2004 it the first open source version of the software was released as MapWindow GIS 3.0, after which it was adopted by the United States Environmental Protection Agency as the primary GIS platform for its BASINS (Better Assessment Science Integrating Point and Nonpoint Sources) watershed analysis and modeling software.

[3] As the project has grown, much of the day-to-day management of the code and associated website has been handled by Paul Meems and a group of volunteer user-developers from around the world.

[4] A user manual for MapWinGIS ActiveX Control written by Daniel P. Ames and Dinesh Grover was released through in 2007.

Updates for MapWindow GIS are regularly released by a group of student and volunteer developers.