Excess sediment and nutrients including nitrogen and phosphorus are major causes of non-point source (NPS) pollution in rivers and streams draining agricultural watersheds. Research studies indicate that a significant proportion of NPS pollutants entering the Mississippi River comes from agricultural watersheds in the Midwest. Illinois watersheds are among those that contribute the highest nutrient flux to the Gulf of Mexico. Watershed Best Management practices (BMPs) could serve as crucial control measures in reducing NPS pollutants from agricultural watersheds and have been applied in many places in Upper Mississippi River basin. This paper presents a coupled optimization-watershed model designed to identify cost-effective placement of BMPs in watersheds that could result in maximized reduction of NPS pollutants such as sediment and nutrients. The coupled model is an interface between the Soil and Water Assessment Tool (SWAT) and the Non-dominated Sorting Genetic Algorithm II (NSGA-II). The computational model was applied to Bray Creek and Frog Alley watersheds, which are tributary watersheds of the Mackinaw River in central Illinois. The BMP of choice to control sediment and nutrient loadings was constructed wetlands because there has been some practical experience in the study watersheds. Simulation results indicate the constructed wetlands appear to be more effective in reducing nutrient loads in both watersheds and the model was able to provide optimal tradeoffs between pollutant reduction and placement cost of constructed wetlands in the watersheds. The coupled model can assist as a decision support tool in prioritizing and targeting areas for BMP placement in the watersheds, resulting in an optimal reduction of pollutants.