In order to discuss the association between the water quality of Chaohu Lake and the resources input in agriculture of the basin, factors that may affect the lake eutrophication are chosen, such as surplus fertilizer, irrigated area with saved water, agricultural films, water and soil loss control and so on. The methods of correlation analysis and stepwise regression are used. Furthermore, a new method, combined with the Technique for Order Preference by Similarity to Ideal Solution (TOPSIS) method, calculating the surplus fertilizer is designed. The results indicate that among various resources input in agriculture of the basin the surplus fertilizer, irrigated area with saved water and agricultural films have a great influence on Chaohu Lake eutrophication. And one year's lag phase between the water quality of Chaohu Lake and the surplus fertilizer is confirmed. Therefore, it is necessary to raise the utilization efficiency of fertilizer, to improve the irrigation way and to decrease the agricultural water consumption in order to conserve resources and to reduce the influence of agricultural production on the water quality of Chaohu Lake.