In Iowa and many other Midwestern states, excess water is removed artificially throughsubsurface drainage systems. While these drainage systems are vital for crop production, nitrogen (N) added as manure or commercial fertilizer, or derived from soil organic matter, can be carried as nitrate-nitrogen (NO3-N) to downstream water bodies. A five-year, five-replication, field study was conducted in north-central Iowa with the objective to determine the influence of seasonal N application as ammonia or liquid swine manure on flow-weighted NO3-N concentrations and losses in subsurface drainage water and crop yields in a corn-soybean rotation. Four aqua-ammonia N treatments (150 or 225 lb-N/acre applied for corn in late fall or as an early season side-dress) and three manure treatments (200 lb-N/acre for corn in late fall or spring or 150 lb-N/acre in the fall for both corn and soybean) were imposed on subsurface drained, continuous-flow-monitored plots. Four-year average flow-weighted NO3-N concentrations measured in drainage water were ranked: spring aqua-ammonia 225 (23 ppm) = fall manure 150 every year (23 ppm) > fall aqua-ammonia 225 (19ppm) = spring manure 200 (18 ppm) = fall manure 200 (17 ppm) > spring aqua-ammonia 150 (15 ppm) = fall aqua-ammonia 150 (14 ppm). Corn yields were significantly greater (p=0.05) for the spring and fall manure-200 rates than for non-manure treatments. Soybean yields were significantly greater (p=0.05) for the treatments with a spring nitrogen application to the previous corn crop.