The introduction of nutrients from chemical fertilizer, animal manure, wastewater, and atmospheric deposition to the eastern Iowa environment creates a large potential for nutrient transport in watersheds. Agriculture constitutes 93 percent of all land use in eastern Iowa. As part of the U.S. Geological Survey National Water Quality Assessment Program, water samples were collected (typically monthly) from six small and six large watersheds in eastern Iowa between March 1996 and September 1997. A Geographic Information System (GIS) was used to determine land use and quantify inputs of nitrogen and phosphorus within the study area. Streamliow from the watersheds is to the Mississippi River. Chemical fertilizer and animal manure account for 92 percent of the estimated total nitrogen and 99.9 percent of the estimated total phosphorus input in the study area. Total nitrogen and total phosphorus loads for 1996 were estimated for nine of the 12 rivers and creeks using a minimum variance unbiased estimator model. A seasonal pattern of concentrations and loads was observed. The greatest concentrations and loads occur in the late spring to early summer in conjunction with row-crop fertilizer applications and spring nmoff and again in the late fall to early winter as vegetation goes into dormancy and additional fertilizer is applied to row-crop fields. The three largest rivers in eastern Iowa transported an estimated total of 79,000 metric tons of total nitrogen and 6,800 metric tons of total phosphorus to the Mississippi River in 1996. The estimated mass of total nitrogen and total phosphorus transported to the Mississippi River represents about 19 percent of all estimated nitrogen and 9 percent of all estimated phosphorus input to the study area.