Water quality and yield in the Upper Mississippi River Basin (UMRB) are critically important for the economic and environmental well-being of the US Midwest. For example, the UMRB constitutes a minor portion (15%) of the Mississippi River Basin, but is recognized as a major contributor (56%) of the nitrogen loadings transported to the Gulf of Mexico. The impacts of climate change on the UMRB water quality and quantity will have significant long-term implications of the region. In our previous projects we have constructed two 10-year simulated climates for the US corresponding to current and future scenario climates at 50-km horizontal resolution, roughly the scale of 7-digit basins. In this study we use regional climate model generated climates to drive the Soil Water Assessment Tools (SWAT) model over the entire UMRB. SWAT is a watershed scale model developed to predict impact of land management practices on water, sediment, and agricultural chemical movement in large complex watersheds with varying soils, land use, and management conditions over long periods of time. Water quality and discharge will be compared between the current and scenario simulations, with emphasis on extreme events and interannual variability of hydrological cycles. In particular, some common hydrological budget terms (e.g., runoff, evaporation, etc.) from SWAT will be examined against those in the climate model as a means of ensuring compatibility in climate-hydrological model coupling.