Riverine nitrate N in the Mississippi River leads to hypoxia in the Gulf of Mexico. Several recent modeling studies estimated major N inputs and suggested source areas that could be targeted for conservation programs. We conducted a similar analysis with more recent and extensive data that demonstrates the importance of hydrology in controlling the percentage of net N inputs (NNI) exported by rivers. The average fraction of annual riverine nitrate N export/NNI ranged from 0.05 for the lower Mississippi subbasin to 0.3 for the upper Mississippi River basin and as high as 1.4 (4.2 in a wet year) for the Embarras River watershed, a mostly tile-drained basin. Intensive corn (Zea mays L.) and soybean [Glycine max (L.) Merr.] watersheds on Mollisols had low NNI values and when combined with riverine N losses suggest a net depletion of soil organic N. We used county-level data to develop a nonlinear model ofN inputs and landscape factors that were related to winter-spring riverine nitrate yields for 153 watersheds within the basin. We found that river runoff times fertilizer N input was the major predictive term, explaining 76% of the variation in the model. Fertilizer inputs were highly correlated with fraction of land area in row crops. Tile drainage explained 17% of the spatial variation in winter-spring nitrate yield, whereas human consumption of N (i.e., sewage effluent) accounted for 7%. Net N inputs were not a good predictor of riverine nitrate N yields, nor were other N balances. We used this model to predict the expected nitrate N yield from each county in the Mississippi River basin; the greatest nitrate N yields corresponded to the highly productive, tile-drained cornbelt from southwest Minnesota across Iowa, Illinois, Indiana, and Ohio. This analysis can be used to guide decisions about where efforts to reduce nitrate N losses can be most effectively targeted to improve local water quality and reduce export to the Gulf of Mexico.