With nearly 95 percent of the basin's land mass applied to agriculture, non-point source pollution is a major contributor to the contamination in the river and its floodplain. Erosion of farmland soils as well as direct rainfall runoff can introduce fertilizers and a variety of pesticides, principally organochlorine products, into the bottomland ecosystem. These substances may be toxic both through direct exposure as well as through bioaccumulation in the food chain with secondary effects on reproduction and behavior. Since 1967, the U.S. Fish and Wildlife Service periodically monitors organochlorine residues in fish samples from across the nation and have shown that persistent pesticides such as aldrin, endrin, dieldrin, DDT, and chlordane are found in significant levels in Missouri River fish. The presence of heavy metals such as mercury, selenium, copper, and cadmium in sediments and fauna of the Missouri River and its tributaries have been documented over the years.
Many metals are essential elements for life needed in minute amounts by organisms.
Metal concentrations in excess can inhibit reproduction, decrease growth, and reduce survival. Past mining activities, industrial discharge and natural occurrences have been identified as sources of these heavy metals. These permits are associated with publicly-owned water and sewage treatment facilities and industrial discharges. Many pipelines cross states transporting natural gas, crude oil and petroleum products and transverse the Missouri River and its tributaries. In 1988 and 1990 there were breaks in pipelines releasing petroleum products into the Gasconade and Chariton Rivers, respectively, which ultimately ended up in the Missouri River.