Long-term applications of organic or inorganic sources of N to croplands can increase the leaching potential of nitrate–nitrogen (NO3–N) for soils underlain by subsurface drainage “tile” network. A field study was conducted for 6 years (1993–1998) to determine the effects of liquid swine manure and urea ammonium nitrate (UAN) solution fertilizer applications on NO3–N concentrations and NO3–N losses with subsurface drainage water under continuous corn (Zea maize L.) and corn after soybean (Glycine max. L.) production systems. The field data collected at Iowa State University's northeastern research center near Nashua, Iowa, under six N-management treatments and each replicated three times, were analyzed as a randomized complete block design. The flow weighted average (FWA) NO3–N concentrations in tile flow were affected significantly (P < 0.05) by N-application rates from swine manure, growing season and treatment effects. Peak (FWA) NO3–N concentrations values of 31.8 mg L−1 under swine manure and 15.5 mg L−1 under UAN in subsurface drain water were observed in 1995 following the dry year of 1994. The 6-year average crop rotation effects on NO3–N losses with tile flows were not found to be significantly affected either with swine manure or UAN-fertilizer applications but showed significant increase in corn grain yields under both the systems. Liquid swine manure, averaged across the 6-year period, resulted in significantly (P < 0.05) greater NO3–N losses with tile flows by 53% (26 kg N ha−1 versus 17 kg N ha−1) and showed no difference in corn grain yields in comparison with UAN-fertilizer applications under continuous corn production system. These results emphasize the need for better management of swine manure application system during the wet and dry growing seasons to reduce NO3–N leaching losses to shallow groundwater systems to avoid contamination of drinking water supplies.