SPAtially Referenced Regressions On Watershed attributes (SPARROW) models were used to relate instream nutrient loads to sources and factors influencing the transport of nutrients in the Missouri River Basin. Agricultural inputs from fertilizer and manure were the largest nutrient sources throughout a large part of the basin, although atmospheric and urban inputs were important sources in some areas. Sediment mobilized from stream channels was a source of phosphorus in medium and larger streams. Irrigation on agricultural land was estimated to decrease the nitrogen load reaching the Mississippi River by as much as 17%, likely as a result of increased anoxia and denitrification in the soil zone. Approximately 16% of the nitrogen load and 33% of the phosphorus load that would have otherwise reached the Mississippi River was retained in reservoirs and lakes throughout the basin. Nearly half of the total attenuation occurred in the eight largest water bodies. Unlike the other major tributary basins, nearly the entire instream nutrient load leaving the outlet of the Platte and Kansas River subbasins reached the Mississippi River. Most of the larger reservoirs and lakes in the Platte River subbasin are upstream of the major sources, whereas in the Kansas River subbasin, most of the source inputs are in the southeast part of the subbasin where characteristics of the area and proximity to the Missouri River facilitate delivery of nutrients to the Mississippi River.