Based on Delft3D model, a two-dimensional hydrodynamic model was established and validated against data of polluted water cluster in 2007 for Taihu Lake. Then hydrodynamic diffusion numerical experiments were performed to compare and analyze the diffusion of polluted water cluster under SE 3 m·s-1 wind condition with different water diversion measures. The simulated results show that the larger drawing flow from Wangyu River, the better effect on pollution diluted near Gonghu Waterworks in northern Taihu Lake, however larger draining flow to Taipu River has little influence there.As for geographic location and recharged water source, new water intake of Gonghu Waterworks is better than the old one.