Eutrophication is a serious water pollution problem in many lakes and reservoirs. One method of understanding the causes of eutrophication and devising strategies to address this phenomenon is watershed modeling. An integrated model is developed in this paper for simulating and evaluating the water quality protection strategies of reservoirs based on controlling the upstream point and non-point sources of pollution and also reservoir operation. To achieve this, Soil and Water Assessment Tool (SWAT) model is used for modeling of the surface runoff and transportation of pollutant load over the watershed area and then, the numerical model CE-Qual-W2 is used for simulating the reservoir water quality. These models are linked to simulate the transmission and distribution of water quality variables in the Seimare watershed-reservoir system, west part of Iran. After calibration of the models, different strategies for reduction of pollution over the watershed are simulated and ranked based on their efficiency in reducing the pollution load entering into the reservoir. Results show that completion and modernization of the sewage network and wastewater treatment plant of Kermanshah city as long as adopting some measures against the direct release of municipal wastewater into the Gharehsou River can reduce the pollution load by 40-50% as the best short term strategy. It is also found that in the long-term period, watershed management and decreasing local animal husbandry activities are the most effective measure for reducing the nutrient load entering Seimare reservoir, and thus need to be considered in the future watershed management policies and programs.