Miyun Reservoir is the main surface source of drinking water for Beijing, China. Water eutrophication has compelled authorities to improve the water quality in its upstream catchment. However, a water-quality survey of the entire catchment was lacking. A total of 52 monitoring sites covering the entire catchment were sampled approximately monthly from July–September 2013, in response to rainfall and runoff. Six water nutrient concentrations were used to characterize the eutrophication, which was relatively severe. The total nitrogen pollution was classified as the worst grade of the water-quality standard. The water quality of Bai River was superior to that of Chao River, while the quality of tributaries was better than that of main rivers. The upstream and downstream reaches of main rivers and small tributaries usually had cleaner water than the middle reaches. The worst pollution mainly appeared in the middle reaches in Hebei Province. Spatial variations in water quality were closely related to land use quantitative characteristics of sub-watersheds. We suggest that a balanced, transparent compensation mechanism focused on Hebei Province would assist to improve water quality.