According to the observed data, this paper analyzed the water diversion allocation in the West Lake. The result shows that the total phosphorus concentration tends to homogenization effect after the allocation changing. A two-dimensional hydrodynamic numerical model for water quality was set up to test the planar distribution of the total phosphorus concentration in the West Lake. This paper also analyzed the rational allocation of the inlets and outlet water diversion scheme how to improve the flow field of the West Lake and how to decrease the total phosphorus concentration.