Water quality deterioration and eutrophication have become a global concern, while reservoir pollution caused by multiple factors has led to frequent algal blooms, posing a serious threat to rural drinking water security and urban water supply. The purpose of this paper is to analyze the current water quality of Waihu Reservoir and use the single index method, the weighted comprehensive scoring method, and the nutrient level index method (TLI) to evaluate eutrophication. On this basis, the pollution sources of the reservoir are comprehensively analyzed and discussed, and effective control strategies are proposed. The evaluation results indicate that the reservoir is of moderate eutrophication type. Therefore, reducing the input of nutrients such as nitrogen and phosphorus in water is the main goal of alleviating exogenous pollution. The combination of engineering intervention and ecological restoration strategies to remove nutrients from the aquatic environment is an effective strategy to manage endogenous pollution. From the point of view of the source of pollution, this study provides an in-depth analysis of exogenous and endogenous pollution, respectively, and the proposed treatment is instructive for the control and routine management of eutrophication in the Waihu Reservoir, as well as for the management of similar problems in different reservoirs.