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There are lots of lakes with shallow depth and slow water velocity all over the Suzhou city. The aquatic environment of these lakes become more and more worse because of the development of urbanization. In order to predict the lake eutrophication, it is necessary to know the nutrients distribution such as phosphorus and nitrogen pollution. It takes the depth- averaged two dimensional water quality model to simulate aquatic environment system including hydrodynamical movement and transport of nutrient material in the large lake(Chenghu lake) with important functions. A comprehensive decay parameter of pollutant confirmed by field data is introduced in the calculation, which synthetically considers the settlement velocity and release speed of nitrogen and phosphorus at the same time. The result of simulation shows the distribution rules and characteristics of nutrients, and also shows that the main contamination comes from the runoff of the Wusong River which is in the west of the lake. These results should be significant to prevent and predict the lake eutrophication.