A long-term study (1998 to 2009) was initiated on eleven tile-drained field plots, ranging in size from 0.19 to 0.47 ha, to investigate the effects of poultry manure application on subsurface drainage water quality in Iowa under a corn-soybean rotation system. The experimental treatments included poultry manure at rates of 168 kg N ha-1 (PM) and 336 kg N ha-1 (PM2), each with three replications; nitrogen application from chemical fertilizer, urea ammonium nitrate (UAN), at a rate of 168 kg N ha-1 with four replications; and a control treatment that received 0 kg N ha-1. Subsurface drainage (tile) flow volume was monitored, and drainage samples were collected and analyzed for nitrate-nitrogen (NO3-N). The results from this 12-year study show that NO3-N losses with tile drainage were more likely to occur during the early stages of crop production (April to June) and were more related to the monthly distribution of precipitation than the total rainfall amount. The overall results of this study indicate that applying poultry manure at 168 kg N ha-1 resulted in significantly lower flow-weighted nitrate concentrations (PM < UAN < PM2) and the lowest nitrogen losses to subsurface drain water compared to UAN and PM2 application(PM < UAN < PM2), as well as higher crop yields compared to UAN application. Therefore, it can be concluded that poultry manure application at a rate of 168 kg N ha-1 is an environmentally sound N application practice with good yield potential for corn and soybean production systems with poorly drained soils in the upper Midwest. Future work is recommended to identify new practices and technologies to reduce nitrate loss to water systems.