Excess precipitation in Iowa and many other agricultural production areas is removed artificially via subsurface drainage systems that intercept and usually divert it to surface waters. Nitrogen, either applied as fertilizer or manure and derived from soil organic matter, can be carried as nitrate with the excess water in quantities that can cause deleterious effects downstream. A four-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 3-5% organic matter. The objective was to determine the influence of seasonal N application and the use of nitrapyrin [inhibitor; 2-chloro-6 (trichloromethyl) pyridine] on flow-weighted nitrate-nitrogen concentrations and yields in a corn-soybean rotation, combined on single plots. Six aqua-ammonia nitrogen treatments (168 and 252 kg/ha at planting and in late fall, and 168 kg/ha at planting and late fall with nitrapyrin) were imposed on subsurface drained, continuous-flow-monitored plots. Combined fall 1999 and spring 2000 precipitation was 42% of normal average. Subsequently, normal precipitation was recorded for both fall and spring periods (after fall application, and before spring application) until spring and fall 2002 (51% and 73% of normal, respectively). Spring 2003 precipitation was again only 51% of normal average. Four-year average, flow-weighted nitrate-nitrogen concentrations ranked in highest to lowest order: spring-252(22.9 mg/L;a) > fall-252(18.1 mg/L;b) > spring-168 w/inhibitor(17.7 mg/L;bc) > fall-168 w/inhibitor(16.0 mg/L;bcd) > spring-168(14.8 mg/L;cd) > fall-168(14.2 mg/L;cd). Spring application plots had significantly greater soybean yield the following season compared to fall applications. Greatest corn yields were observed for the spring-252 and fall-168 rates, but were only significantly different than the spring-168 rate for yield. Therefore, under slightly dry to normal precipitation conditions, corn yields and nitrate-nitrogen concentrations in subsurface drainage were not significantly different between seasonal timing or inhibitor use treatments at the 168 kg/ha nitrogen rate.