Nitrogen budget calculations performed for highflow and low-flow years in the major sub-basins of the Upper Mississippi River watershed show differences in nitrogen applications and discharges. Nitrogen budgets show that fertilizer is the most important input of nitrogen to the basins, but also show that atmospheric input and animal manures can be significant inputs of nitrogen to the basins. The transport of nitrogen from the land to rivers varies with the prevailing hydrologic conditions. The annual nitrogen budgets are not balanced. In years of high precipitation and river discharge, more nitrogen can be removed than had been applied that year, presumably from N stored in the soil or ground water. Storage of nitrogen in soils is a major unknown in the model, but calculations suggest that it is a significant reservoir of N.