Abstract: The Chenhang reservoir, Qingcaosha reservoir and Dongfengxisha reservoir are the three major water sources at the Yangtze River estuary. 80% of the Shanghai's drinking water comes from the three major water sources. The intrusion of the salt water in the low flow seasons is always a great threat to the water source safety at the Yangtze River estuary. As the two main dynamics forces of the estuarine area, it is necessary to further study the influences of runoff and tide on the salt water intrusion to the water sources in the Yangtze River estuary. A two-dimensional salt transport numerical model is developed to simulate the flow-salt dynamic processes. And the relationship between the salinity hydrograph and the tidal line can be taken as an important basis for analyzing the influences of the northern branch on the water sources. The analyses of the model results show that the characteristics of the salinity duration lines are different because of the different locations of the three water sources. The relationship between the salinity and water level duration can indicate the degree affected by saltwater spilling over from the north branch and saltwater directly from the sea. While the salt water spilling over from the north branch occurs, the water sources of the Dongfengxisha reservoir, the Chenhang reservoir and the Qingcaosha reservoir are most seriously affected by the brine in the spring, middle and lower tides respectively. With the increase of runoff volume, the time affected by saltwater intrusion will advance, but the salinity will decrease with the increase of the runoff.