In order to control the effluent discharge of the Shaying River more effectively and to ensure the normal operation on the water diversion project on the Xifei River line, a one-dimensional hydrodynamic-water quality coupling model was established from MIKE11, and the degradation and dilution characteristics of pollutants in the process of sewage effluent discharge were analyzed in terms of the mechanism of the influence on the water quality of the water-intake of Xifei River, using ammonia nitrogen as the water quality index. The results show that before flood, with the increase in the ratio of feeder flow, the pollution mass transitions from being mainly subject to degradation to dilution and the effluent discharged at the beginning of the flood mainly relies on the dilution effect of the main stream to reduce the concentration. When the sewage flow of the Shaying River before and at the beginning of the flood is greater than that of the main stream by 10% and 7%, respectively, the water quality at the water intake is at risk of exceeding Class III of surface water standard. There is a power function relationship between the concentration of ammonia nitrogen at the intake and the branch to trunk flow ratio, and the fitting effect of the two is related to the degree of dilution of the polluted mass by the main stream.