As climate changes, the uncertainty of water availability, changing magnitudes of nonpoint source pollution, and uncertainty of BMP effectiveness are issues that watershed managers and stakeholders must consider and plan for. The objective of this study was to determine how best management effectiveness will be affected by climate change using the Soil and Water Assessment Tool. Using downscaled monthly precipitation and temperature data output from the Community Climate System Model (CCSM) provided by the NCAR GIS Initiative Climate Change Scenarios, daily precipitation and temperature data was produced based on observed weather station data for the Tuttle Creek Lake watershed in Kansas and Nebraska. The A1B, A2, and B1 SRES emissions scenarios were compared to historical CCSM model output. Seven agricultural BMPs were physically represented within SWAT and compared across climate scenarios: contour farming, grazing management, native grass, porous gully plugs, conservation tillage, no-tillage, and terraces. Water yield (up to 69%), surface runoff (up to 61%), sediment load (up to 74%), nitrogen load (up to 66%), and phosphorus load (up to 61%) increased in all three climate scenarios. Terraces and contour farming were determined to be the most effective in pollution reduction at the field and watershed scale in future scenarios, while porous gully plugs and conservation tillage showed no significant changes in pollution load or percent reduction and had reduction efficiencies close to 0%. Grazing management, no-tillage, and grazing management percent and load reduction in future scenarios varied at the field and watershed scale. This study demonstrates that BMP performance in terms of sediment, nitrogen, and phosphorus reduction significantly changes in future climate scenarios at the field scale, while performance generally does not change significantly at the watershed scale.