In this paper, we take the Qinhuai River Basin in Nanjing as an example to study the influence of diversion flow ratio on water environment. The daily precipitation of 20 rainfall stations in the basin was collected from 1962 to 2006, and the rainfall under different assurance rates was calculated by P-III frequency curve to calculate the surface runoff at different typical years. In the meantime, according to the downstream furcated estuary water level at different typical years, the diversion flow ratio under different frequency is calculated by using the mathematical model of water environment. The results show that the diversion flow ratio of a branch channel increases with the increase of water level difference, and the growth rate decreases gradually. The other branch channel diversion flow ratio decreases with the increase of water level difference, and the decreasing rate decreases gradually. The pollutant concentration in the bifurcated rivers are equal, but the concentration decreases exponentially with the increase of the upstream flow. Under different rainfall frequency, the diversion pollutant ratio and diversion flow ratio are equal at different months of different years.