MWSWAT is a plugin for MapWindow, an Open Source GIS system available from http://www.mapwindow.org which runs under the Windows operating system. The MWSWAT plugin, which is also open source, is downloaded as a Windows installer.
Install MapWindow first, then run the MWSWAT installer. MWSWAT will appear in the Plug-ins menu the next time you start MapWindow.
You will also need to download and install the SWAT Editor, also available from the SWAT web site. With the current version 2.2 of MWSWAT you need version 2.1.5 or later of the SWAT Editor. Install it by unzipping and running Setup. Use the default installation folder so that MWSWAT can find it.
Two example watersheds have been created, San Juan in Mexico and Linthipe in Malawi. Initial geo-processing for these watersheds is described in the geo-processing document, and the use of MWSWAT to set up and run SWAT on them is described in the MWSWAT tutorial document, both on the documents page. The other resources, maps and weather generator files, that you need for them are in two zip archives:
The source code is available from the MapWindow subversion repository at http://svn.mapwindow.org/svnroot/MapWindow4Plugins/MWSWAT. This is best accessed by a tool like Tortoise.