The increased use of nitrogen (N) fertilizers in the Mississippi Basin since the 1950s is partially responsible for an increase in crop production, but also a massive increase in nitrate export by the Mississippi River. We used the IBIS terrestrial ecosystem model, including new maize and soybean submodels, and the HYDRA hydrological transport model to investigate the role of climate variability, land cover and N-fertilizer application on crop yield, N cycling and nitrate export in the Upper Mississippi Basin from 1974--1994. Simulated annual mean maize and soybean yields were both within 20% of USDA historical estimates in over 80% of the crop-growing counties. There was also strong agreement between simulated and USGS estimated annual nitrate export for the Mississippi River at Clinton, Iowa (r2 = 0.81), the outlet of the basin, and the Minnesota River at Jordan, Minnesota (r2 = 0.78). The model also indicated a 30% increase in N-fertilizer application across the basin would have caused only a 4% increase in mean maize yield, but a 53% increase in mean dissolved inorganic nitrogen (DIN) leaching, while a 30% decrease in N-fertilizer application would have caused a 10% decrease in maize yield, but a 37% decrease in DIN leaching. At higher levels of N-fertilizer usage, nitrate export becomes increasingly sensitive to the hydrologic conditions, particularly when there is ample residual N in the soil. Therefore any effort to reduce nitrate export without significantly affecting crop yields would have to account for previous soil-N conditions and climate variability.