Abstract: In order to develop the Yangtze River Estuary in an orderly way, control the layout of water intake and sewage outlet along the Yangtze River and ensure the safety of the water source, according to the Yangtze River Estuary water environment bearing capacity, water function zones and water quality model analysis results, the Yangtze River Estuary waters is divided into water intake area and sewage outlet area and the plan and adjustment scheme of the water intake and sewage outlet are put forward. The layout and the strategic plan of the water source area in the Yangtze River Estuary are proposed. The study shows that it is important to protect the water environment of Yangtze River estuary by rationally arranging water intake and sewage outlet and reducing the pollutant load of land into the Yangtze River. Adherence to the principle of "two rivers complement each other" is a long-term strategy of water sources in Shanghai. Improving the Yangtze River estuary water source plan is very important to the sustainable development of Shanghai and Yangtze River Economic Belt.