SWAT is acronym for Soil and Water Assessment Tool and it is river basin, or watershed scale model developed in USDA Agriculture Research Service. SWAT was developed to predict impact of land management practices on water, sediment and agriculture chemical yield in large complex watersheds with varying soil, land use and management condition over long period of time.
More about SWAT you can find on link http://swat.tamu.edu/
What is interested for SWAT is that it is free, well tested and now implemented in QGIS as plugin. Also, there is link for MODFLOW.
If you want to see practical example of SWAT simulation for 1800 km2 watershed in Europe just cintact me on email advancedgwt@gmail.com and I will organize 15 minute presentation via Skype.