Spatiotemporal characteristics of water environment in Beijing were studied at the watershed scale to comprehensively analyze the water environment status of the watershed. The results show a pronounced spatiotemporal heterogeneity of water environment quality in the Beijing watershed. The surface water quality in the upstream was significantly better than that in the downstream. After the surface water flowing through the central urban area, the water quality began to deteriorate, indicating that the central urban area was the main source of watershed pollution. The inter-month fluctuation of surface water quality categories from 2018 to 2019 was notable, which indicated that the surface water bodies had not continued to be improved. It was mainly caused by the combined factors of non-point and point source pollution input from upland area, the release of internal pollution as well as the lack of river ecological environment water. In the end, comprehensive management measures of watershed in Beijing were proposed including enhancing the source control of watershed, comprehensively promoting the construction of sponge city in central urban area, continuously increasing the supply of river ecological environment water, exploring effective introduction mechanism of water environment management market, intensifying comprehensive and collaborative management of the watershed water environment and so on.