Non-point source (NPS) pollution, including fertilizer and manure application, sediment erosion, and haphazard discharge of wastewater, has led to a wide range of water pollution problems in the Miyun Reservoir, the most important drinking water source in Beijing. In this study, the Soil and Water Assessment Tool (SWAT) model was used to evaluate NPS pollution loads and the effectiveness of best management practices (BMPs) in the two subwatersheds within the Miyun Reservoir Watershed (MRW). Spatial distributions of soil types and land uses, and changes in precipitation and fertilizer application, were analysed to elucidate the distribution of pollution in this watershed from 1990 to 2010. The results demonstrated that the nutrient losses were significantly affected by soil properties and higher in both agricultural land and barren land. The temporal distribution of pollutant loads was consistent with that of precipitation. Soil erosion and nutrient losses would increase risks of water eutrophication and ecosystem degradation in the Miyun Reservoir. The well-calibrated SWAT model was used to assess the effects of several Best Management Practices (BMPs), including filter strips, grassed waterways, constructed wetlands, detention basins, converting farmland to forest, soil nutrient management, conservation tillage, contour farming, and strip cropping. The removal rates of those BMPs ranged from 1.03 to 38.40% and from 1.36 to 39.34% for total nitrogen (TN) and total phosphorus (TP) loads, respectively. The efficiency of BMPs was dependent on design parameters and local factors and varied in different sub-basins. This study revealed that no single BMP could achieve the water quality improvement targets and highlighted the importance of optimal configuration of BMP combinations at sub-basin scale. The findings presented here provide valuable information for developing the sustainable watershed management strategies.