Sudden water pollution accidents may seriously affect the intake of water source, and the establishment of early warning stations is very important to protect the safety of water source. The existing research has not systematically discussed the determination method of early warning stations of water source in tidal river reach. Based on the coupled mathematical model of hydrodynamic and water quality in the Chengtong tidal reach of the Yangtze River, and on the basis of clarifying the law of diffusion and transport of pollutants in the reach under the combined action of channel and tide, the location and number of early warning stations in the Changqingsha and Langshan water sources were preliminarily established. Combined with the distribution characteristics of potential pollution sources and the accumulation characteristics of pollutants affecting the water source, the early warning station was checked in space, and the early warning station was checked in time by using the timeliness of early warning response. The locations of four early warning stations upstream and downstream of the two water sources were finally determined. Based on the correlation of water quality index between warning station and water source, the emergency response scheme of water source and the risk response limit value for phenol leakage in these two water sources were determined.