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Climate change, in terms of changes in temperature and patterns of precipitation, has significant impacts on water resources and watershed ecosystems. Adapting to climate change is becoming an important strategy for watershed management. The goal of this study was to quantify the impacts of climate change on watershed hydrological processes and water quality, to evaluate the efficiency of Best Management Practices (BMPs) and the possible effects of a changing climate, and to configure cost-effective BMPs at sub-basin scale using a multi objective optimization method to mitigate climate effects on water resource. The Soil and Water Assessment Tool (SWAT) model was used to simulate the possible effects of changing climate on watershed hydrological and water-quality processes and adaptation options in the Miyun Reservoir Watershed (MRW). Climate change had significant impacts on water balance components such as precipitation, runoff, and evapotranspiration (ET) and on water-quality components such as sediment and nutrient loads. A substantial decreasing trend of runoff indicated that the Miyun Reservoir faced a more acute challenge of insufficient water-supply capacity. Compared with baseline climate, climate change represented by precipitation and temperature regimes resulted in substantial increases in sediment load (12.95%) and nutrient losses (7.26% for TN and 9.56% for TP) on average all sub-basins. Climate variability had significant effects on BMP efficiency through effects on watershed hydrology, soil erosion, and nutrient losses. Results highlight the importance of optimal configuration of site-specific BMPs at sub-basin scale for adaptation to climate change. The methods and findings presented here hold promise to enhance the resilience of the watershed system to current and future climate change.