Most agricultural reservoirs in Korea are more than 50 years old, have low water depth and storage capacity, and have experienced contaminant deposition for decades. Contaminated sedimentation on the reservoir bottom can cause water pollution and eutrophication. Consequently, intervention is required to remove and manage the sediments. We analyzed the release characteristics of organic matter and nutrients from sediments of four reservoirs to predict the pollution caused by sediment release and investigated their effects on water quality. Additionally, the effects of sediment release were compared with those of influent pollutant loads to the reservoirs. We employed the core culture method to determine the release concentrations changes under oxic, anoxic, and control conditions in the collected sediments. In all the studied reservoirs, the release concentrations of nitrate nitrogen increased under oxic conditions and those of ammonia nitrogen, total phosphorus, and phosphate phosphorus increased under anoxic conditions. The water quality was affected by sediment release from the reservoir bottom. The release fluxes (internal sources) of total nitrogen and total phosphorous for the influent pollutant loads (external source) were 2.3–43.7% and 24.9–48.1%, respectively, for each reservoir. Therefore, optimal pollution control and management strategies will depend on the characteristics of individual reservoirs.