Based on the water quality data of Shenzhen Bay, Pearl River Estuary, tail water of water purification plant, non-point source and interception and drainage overflow water in the study area, the spatio-temporal distribution characteristics of water quality and pollutant sources in Shenzhen Bay are systematically analyzed. Results show that the current water quality of Shenzhen Bay is not up to standard, and the key pollution factors are inorganic nitrogen(DIN)and active phosphate(DIP). The water quality in rainy seasons is generally inferior to that in dry seasons, and the water quality in the inner bay is obviously inferior to that in the outer bay. The approaches of pollutants entering Shenzhen Bay include: 6 estuaries(Houhai River, Dasha River, Xiaosha River, Fengtang River, Xinzhou River, Shenzhen River), 1 sewage outlet(tail water outlet of Futian water purification plant), 34 rainwater outlets and Shenzhen Bay outlet. After water environment treatment measures such as wastewater collection in dry season and tailwater upgrading, the main pollution sources of Shenzhen Bay are non-point source and interception and drainage overflow pollution. The concentration of nitrogen and phosphorus nutrients in the bay can reach the class V of national standard of surface water, which is 5~15 times of the current water quality of Shenzhen Bay. In the rainy season, the total load of nitrogen and phosphorus from non-point sources and intercepted and discharged overflow pollution reaches 76. 2 t and 283. 8 t. This has a serious impact on the water quality of Shenzhen Bay, which has no residual capacity of nitrogen and phosphorus nutrients.