The response of a corn-soybean rotation system receiving fall manure application to both corn and soybean is not well understood in terms of its impact on nitrate leaching to subsurface drainage water and crop yields. This field study was conducted from 2001 through 2005 with the key objective of determining the effects of manure application to both corn and soybean on NO3-N concentrations in subsurface drainage water and corn-soybean yields. The study was conducted on 0.4 ha plots instrumented with state-of-the-art subsurface drainage monitoring systems at the Iowa State University research center, Nashua, Iowa. Nitrogen application rates from liquid swine manure averaged 174 and 219 kg N ha-1 to both years of the corn and soybean production system, respectively, compared with 177 kg N ha-1 to corn years only. Field data collected on subsurface drainage, NO3-N concentrations, and leaching losses to subsurface drainage water and crop yields were analyzed as a randomized complete block design. The results indicated that the average flow-weighted NO3-N concentrations and leaching losses increased by more than 50% when manure was applied to both corn and soybean in comparison with manure application to corn only, while yield differences were less than 4%. These results suggest that fall manure application to both corn and soybean is likely to increase NO3-N leaching to shallow groundwater without resulting in significant yield benefits. The increased NO3-N leaching was primarily due to larger total N application from manure to both corn and soybean under the corn-soybean production system studied at this site.