Based on the two-dimensional hydrodynamic model,the two-dimensional water quality model is presented in this paper.According to the numerical simulation and analysis of water environment quality at different frequency floodwater,it concludes that the flood runoff is the first factor for the water environment quality,and points out that the water environment quality is better in low frequency flood than that in high frequency in respect of organic contamination,in addition,the concentration of heavy metal in high frequency flood tends to be increased greatly.