Large water-sample sets collected from 1899 through 1902, 1907, and in the early 1950s allow comparisons of pre-impoundment and post-impoundment (1969 through 2008) nitrogen concentrations in the lower Missouri River. Although urban wastes were not large enough to detectably increase annual loads of total nitrogen at the beginning of the 20th century, carcass waste, stock-yard manure, and untreated human wastes measurably increased ammonia and organic-nitrogen concentrations during low flows. Average total-nitrogen concentrations in both periods were about 2.5 mg/l, but much of the particulate-organic nitrogen, which was the dominant form of nitrogen around 1900, has been replaced by nitrate. This change in speciation was caused by the nearly 80% decrease in suspended-sediment concentrations that occurred after impoundment, modern agriculture, drainage of riparian wetlands, and sewage treatment. Nevertheless, bioavailable nitrogen has not been low enough to limit primary production in the Missouri River since the beginning of the 20th century. Nitrate concentrations have increased more rapidly from 2000 through 2008 (5 to 12% per year), thus increasing bioavailable nitrogen delivered to the Mississippi River and affecting Gulf Coast hypoxia. The increase in nitrate concentrations with distance downstream is much greater during the post-impoundment period. If strategies to decrease total-nitrogen loads focus on particulate N, substantial decreases will be difficult because particulate nitrogen is now only 23% of total nitrogen in the Missouri River. A strategy aimed at decreasing particulates also could further exacerbate land loss along the Gulf of Mexico, which has been sediment starved since Missouri River impoundment. In contrast, strategies or benchmarks aimed at decreasing nitrate loads could substantially decrease nitrogen loadings because nitrates now constitute over half of the Missouri's nitrogen input to the Mississippi. Ongoing restoration and creation of wetlands along the Missouri River could be part of such a nitrate-reduction strategy. Published 2013. This article is a U.S. Government work and is in the public domain in the USA.