The upper Midwest is an area of intensive corn and soybean agriculture that is heavily tile drained. This leads to large losses of nitrate to the Mississippi River, and in turn to the Gulf of Mexico. The objective of this study was to evaluate recent N balances in this area, examining relationships to current and projected stream water nitrate export. We used state level agricultural statistics for fertilizer and crop yields from Iowa and Illinois, as well as more detailed state level statistics on all aspects of crop and animal agriculture for Illinois. A non-linear model was used to relate net N inputs to stream nitrate export for the overall Mississippi River. Due to excellent crop yields with steady fertilizer use, net N inputs (fertilizer + fixation minus harvested grain) since 2000 are much lower than the previous 20 year period. Net N inputs have not been this low since the 1950s. For Illinois, recent net N inputs to the state were 140,000 metric tons of N/yr for 2000 to 2004 (10 kg N/ha/yr), compared to 445,000 metric tons/yr for 1980 to 1999 (30 kg N/ha/yr). Stream nitrate export has not yet responded, and the modeled response suggests that long lags are likely important but that stream export should decrease. However, unfavorable weather conditions leading to nitrate leaching in late winter and spring may complicate the response. The recent record and sustained high yields of corn and soybean agriculture have resulted in an ideal opportunity to examine a large scale ecosystem response in stream nitrate export. The response of stream nitrate export has important agricultural policy implications related to Gulf of Mexico hypoxia.