Taking the core area of Yancheng City as an example, the mathematical model of water quantity and quality was constructed. On the basis of the normal water supply scheme, the pollutants entering the river with the initial rainwater runoff were fully considered and the influence of the initial rainwater pollution on the living water effect was analyzed. The results show that the water quality improvement effect of the living water scheme is related to the water quality of diversion water and the distribution of pollutant concentration. When the target of living water is the same, the time of living water considering initial rainwater pollution is longer than that without considering initial rainwater pollution. Due to different confluence time, the peak time and the time of reaching the standard of pollutant concentration in the upstream section are delayed compared with that in the downstream section when the initial rainwater pollution is considered.