Phosphorus is one of the most important and essential mineral nutrients for corn and soybean production. Phosphorus is primarily transported to surface water bodies with surface runoff from agricultural fields as it is strongly absorbed to the soil particles. However, small amounts of dissolved phosphorus lost with subsurface drainage water can be immediately available for accelerating eutrophication in surface water bodies at critical phosphorus concentrations of 10 to 20 gL-1. A long-term subsurface drainage water quality study was conducted at the Nashua research site located in the Northeast part of Iowa, USA. The overall goal of this study was to investigate the effects of the application of swine manure and commercial fertilizer (ammonium nitrate, UAN) on phosphorus leaching to subsurface drainage water under a corn-soybean rotation. Effects of different application timings and rates were also evaluated in this long-term study (2001-2006). The results of this study indicated that phosphorus concentrations in subsurface drain water, from all experimental treatments, were highly variable and not consistent with the amount of phosphorus applied from swine manure and/or fertilizer. Manure applications at higher rates however, resulted in significantly higher phosphorus concentrations (p=0.05) in subsurface drain water in comparison to other treatments in the soybean year. Spring manure applications generally showed lower phosphorous concentration in subsurface drain water in comparison with fall manure applications, although differences were not statistically significant (p=0.05).