The deterioration of water quality due to human-driven alternations has an adverse effect on the environment. More than 50% of surveyed surface water bodies in the United States (US) are classified as impaired waters as per the Clean Water Act. The pollutants affecting the water quality in the US are classified as point and non-point sources. Pollutant mitigation strategies such as the selective implementation of best management practices (BMPs) based on the severity of the pollution could improve water quality by reducing the amounts of pollutants. Quantifying the efficiency of a specific management practice can be difficult for large watersheds. Complex hydrologic models are used to assess water quality and quantity at watershed scales. This study used a Soil and Water Assessment Tool (SWAT) that can simulate a longer time series for hydrologic and water quality assessments in the Yazoo River Watershed (YRW). This research aims to estimate streamflow, sediment, and nutrient load reductions by implementing various BMPs in the watershed. BMPs such as vegetative filter strips (VFS), riparian buffers, and cover crops were applied in this study. Results from these scenarios indicated that the combination of VFS and riparian buffers at the watershed scale had the highest reduction in sediment and nutrient loads. Correspondingly, a comparative analysis of BMP implementation at the field and watershed scale showed the variability in the reduction of streamflow, sediment, and nutrient loads. The results indicated that combining VFS and CC at the field scale watershed had a greater nutrient reduction than at the watershed scale. Likewise, this study investigated the soil-specific sediment load assessments for predominant soils in the YRW, which resulted in soil types of Alligator, Sharkey, and Memphis soils being highly erodible from the agricultural-dominant region. This study also included the effect of historical land use and land-cover (LULC) change on water quality. The analysis revealed that there was a significant decrease in pastureland and a simultaneous increase in forest and wetlands, which showed a decreasing trend in hydrologic and water quality outputs. Results from this study could be beneficial in decision-making for prescribing appropriate conservation practices