Various Best Management Practices (BMPs) have been implemented around the world in order to reduce the nutrient loadings in lakes and reservoirs. This study was conducted in the Atwood and Tappan Lakes watersheds of the Tuscarawas basin of Ohio. The flow and nutrient loadings were monitored for a few years at the various locations of the watershed to develop the Soil and Water Assessment Tool (SWAT). The multi-site SWAT model calibration and validation were accomplished with a reasonable model performance. In the next step, the scenario analysis was conducted in the SWAT model using various BMPs, including filter strips, grass waterways, fertilizer reduction, crop rotation, and cover crops to evaluate their performance in reducing nutrients from the watershed. These BMPs were selected based on active consultation with the local stakeholders, who were engaged in the reduction of nutrient loadings from the watersheds. Since the SWAT model calibration for nutrients was not as good as the hydrologic model calibration, several scenarios of nutrient reduction using BMPs were investigated for several years using both calibrated and uncalibrated SWAT models. We examined all the BMPs in 12 sub-watersheds of Atwood and 10 sub-watersheds of the Tappan Lake watershed. The analysis indicated that the management practices of cover crops (rye) in combination with grass waterways with a 10% fertilizer reduction could minimize the nutrient loading to as high as 88%, without significantly compromising the agricultural yield. However, a 10% fertilizer reduction without any BMPs could reduce nutrients just by 9%. The cover crop (rye) with grass waterways seems to be the most effective in reducing nutrients, whereas, the implementation of a filter strip could be the next effective BMPs to reduce nutrient loadings. By and large, the nutrient reduction achieved through the calibrated model was not significantly different from the uncalibrated model even though the nutrient reduction using the calibrated model was slightly higher for all scenarios than that of the uncalibrated model. Our investigation revealed that monitoring the watershed at a small sub-watershed scale and calibrating the SWAT model for nutrients is a delicate job. This analysis is expected to be helpful for the stakeholders working on the restoration of both watersheds.