In Iowa and many other Midwestern states, excess water is removed artificially through subsurface 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 initiated in the fall of 1999 in Pocahontas County, Iowa, on 0.05 ha plots that are predominantly Nicollet, Webster, and Canisteo clay loams with 3% to 5% organic matter located on glacial till within the Des Moines Lobe. The objective was 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 (168 or 252 kg N ha-1 applied for corn in late fall or as an early season side-dress) and three manure treatments (218 kg N ha-1 for corn in late fall or spring or 168 kg N ha-1 in the fall for both corn and soybean) were imposed on subsurface-drained, continuous flow-monitored plots. Precipitation during the drainage season (March to November) was slightly below the long-term norm (722 mm) for all four years in the study period and ranged from 615 mm in 2001 (85% of normal) to 707 mm (98% of normal) in 2004. Monthly rainfall was highly variable, and subsurface drainage, or the lack thereof, usually mimicked the precipitation patterns. On average, 69% of subsurface drainage occurred in May and June of each year, with lower amounts in April and July. Four-year average flow-weighted NO3-N concentrations measured in drainage water were ranked: spring aqua-ammonia 252 (23 mg L-1) = fall manure 168 every year (23 mg L-1) > fall aqua-ammonia 252 (19 mg L-1) = spring manure 218 (18 mg L-1) = fall manure 218 (17 mg L-1) > spring aqua-ammonia 168 (15 mg L-1) = fall aqua-ammonia 168 (14 mg L-1). Corn yields were significantly greater (p = 0.05) for the spring and fall manure 218 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. Overall, under the slightly dry to normal precipitation conditions of this study, corn yields and NO3-N concentrations in subsurface drainage were not significantly different (p = 0.05) between fall and spring treatments at the 168 aqua-ammonia or 218 kg ha-1 N manure N rates.