Water table management through the use of artificial subsurface drainage systems is of primary importance in humid areas with poorly or somewhat poorly drained soils to maximize agricultural productivity Excess precipitation in Iowa and many other Mississippi/Ohio River watershed agricultural production states is removed artificially via subsurface drainage systems that intercept and usually divert it to surface waters. Agricultural drainage systems have been installed to allow timely seedbed preparation, planting and harvesting and to protect crops from extended periods of flooded soil conditions. The tradeoff of improved subsurface drainage is a significant increase in the losses of nitrate-nitrogen (Gilliam, et al., 1999). Nitrogen, either applied as fertilizer, or manure or derived from soil organic matter, can be carried as nitrate with the excess water in quantities that can cause deleterious effects downstream. The movement of nitrogen from agricultural fields via drainage waters is a major factor in nonpoint source pollution of surface waters and ultimately the Gulf of Mexico where it has been implicated as a cause of the Hypoxic Zone (Mitsch et al., 2001; Rabalais, et al., 1996). The environmental impacts downstream depend on the agronomic practices implemented, as well as the site, crops, soils and climatological factors. In recent years the use of animal manure, particularly liquid swine manure, in place of commercial fertilizer has increased. From this, the objectives of this study were to compare nitrate-nitrogen losses and crop yield from subsurface drained areas treated with liquid swine manure and commercial fertilizer. Described within are results from two phases (1995-1999 and 2000-2004) of research studying the effects of swine manure on drainage water quality.