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Best Management Practices (BMPs) are implemented in a watershed to reduce the amount of non-point source pollutants transported to water bodies. However, an optimization algorithm is required to choose the efficient type, size, and location of BMPs for application in a watershed for improving the water quality. In this study, the Charged System Search, a well-known and powerful meta-heuristic optimization algorithm, as an optimization model and a semi-distributed hydrological model i.e. Soil and Water Assesment Tool (SWAT) were coupled to obtain cost-effective combination of different BMPs. To demonstrate the performance and applicability of the coupled model, it was utilized to Sofichai watershed upstream of the Alavian Reservoir in the northwestern part of Iran to compare four reduction levels of sediment, nitrate nitrogen and phosphate phosphorous loads at the watershed outlet.