Chesapeake Bay jurisdictions are required to develop Watershed Implementation Plans (WIPs) to reduce Non-Point Source (NPS) pollution by sediment, nitrogen, and phosphorus, and meet EPA Total Maximum Daily Loads (TMDLs) for water quality. This study quantifies the potential impacts of climate change on Critical Source Areas (CSAs) and Best Management Practice (BMP) efficiencies, two keys to WIP success, in an agricultural watershed in Maryland. The SWAT model was calibrated for the watershed and subjected to climate scenarios SRES B1, A1B and A2, over mid- and end-century time horizons. Simulation results predict that changed precipitation patterns will produce at least a doubling of CSA areas within the watershed and that, with BMPs designed for current climate, TMDLs will be exceeded by a factor of up to 2.4. For WIPs to be robust against climate change, BMPs must be designed for future climate and community-based, participatory implementation strategies are needed.