Increasing awareness of hypoxia in coastal marine regions across the globe has led to creation of nutrient reduction strategies to protect water resources and organisms living in affected waters. In the Mississippi River Basin, the Governor’s Action Plan has called for a 45% load reduction of both, total nitrogen (N) and total phosphorus (P), to reduce the Gulf of Mexico hypoxic zone to a manageable size. Objectives of this dissertation aimed to determine nutrient reduction efficiencies of low-grade weirs, and to evaluate abundance and composition of microbial communities involved in key processes of denitrification following low-grade weir implementation in the Mississippi Delta. Results of this dissertation evidenced the efficiencies of low-grade weirs to reduce nutrient runoff to downstream waters as a viable BMP. Average median load reductions in N, P, and sediment of -5%, 23%, and 29%, respectively, were determined in ditches with low-grade weirs. Results highlighted more efficient reductions in P and sediment, and greater variability in N reductions during storm events, prompting management considerations toward BMP successes and limitations. Valuable insight towards seasonal nutrient fluxes in agricultural runoff due to spring fertilizer applications, increased rainfall patterns in the winter and spring, and drying-wetting cycles, was also evidenced by the data collected. It was determined that utilizing a three-scale sampling regime was most effective for capturing patterns of microbial community abundance and composition in ditches with low-grade weirs. Preliminary evidence towards weir proximity influencing microbial community abundance, and relationships between microbes and soil carbon and N was also found. Utilizing the three-scale sampling regime, microbial communities in multiple drainage ditches, with and without weirs, were investigated. Outcomes showed that weirs increased soil moisture, which subsequently increased functional gene abundance of 16S rRNA and nirS. Furthermore, weir implementation and associated constructions were not found to directly influence microbial community diversity, abundance, or chemical parameters. Results from this dissertation support the potential benefits of weirs to create suitable environments to physically reduce P and sediment loads and for denitrifying microbes to remediate N from agricultural runoff.