The export of nitrate by the Mississippi River to the Gulf of Mexico has tripled since the 1950s primarily due to an increase in agricultural fertilizer application and hydrological changes. Here we have adapted two physically based models, the Integrated Biosphere Simulator (IBIS) terrestrial ecosystem model and the Hydrological Routing Algorithm (HYDRA) hydrological transport model, to simulate the nitrate export in the Mississippi River system and isolate the role of hydrological processes in the observed increase and interannual variability in nitrate export. Using an empirical nitrate input algorithm based on constant land cover and variability in runoff, the modeling system is able to represent much of the spatial and interannual variability in aquatic nitrate export. The results indicate that about a quarter of the sharp increase in nitrate export from 1966 to 1994 was due to an increase in runoff across the basin. This illustrates the pivotal role of hydrology and climate in the balance between storage of nitrate in the terrestrial system and leaching.