The primary objective of this project was to determine the impact of appropriate rates of swine manure applications to corn and soybeans based on nitrogen and phosphorus requirements of crops, soil phosphorus accumulation, and the potential of nitrate and phosphorus leaching to groundwater. Another purpose of this long-term experimental study was to develop and recommend appropriate manure and nutrient management practices to producers to minimize water contamination potential and enhance the use of swine manure as fertilizer. A third component of this study was to determine the potential effects of rye as a cover crop to reduce nitrate loss to shallow groundwater.