Missouri River
Human impacts

Since river commerce and industrial development began in the 1800s, human activity has severely polluted the Missouri and degraded its water quality. Most of the river's floodplain habitat is long gone, replaced by irrigated agricultural land. Development of the floodplain has led to increasing numbers of people and infrastructure within areas at high risk of inundation. Levees have been constructed along more than a third of the river to keep floodwater within the channel, but with the consequences of faster stream velocity and a resulting increase of peak flows in downstream areas. Fertilizer runoff, which causes elevated levels of nitrogen and other nutrients, is a major problem along the Missouri River, especially in Iowa and Missouri. This form of pollution also affects the upper Mississippi, Illinois and Ohio Rivers. Low oxygen levels in rivers and the vast Gulf of Mexico dead zone at the end of the Mississippi Delta are both results of high nutrient concentrations in the Missouri and other tributaries of the Mississippi.

Channelization of the lower Missouri waters has made the river narrower, deeper and less accessible to riparian flora and fauna. Many dams and bank stabilization projects have been built to help convert 300,000 acres (1,200 km) of Missouri River floodplain to agricultural land. Channel control has reduced the volume of sediment transported downstream by the river and eliminated critical habitat for fish, birds and amphibians. By the early 21st century, declines in populations of native species prompted the U.S. Fish and Wildlife Service to issue a biological opinion recommending restoration of river habitats for federally endangered bird and fish species.

The USACE began work on ecosystem restoration projects along the lower Missouri River in the early 21st century. Because of the low use of the shipping channel in the lower Missouri maintained by the USACE, it is now considered feasible to remove some of the levees, dikes, and wing dams that constrict the river's flow, thus allowing it to naturally restore its banks. By 2001, there were 87,000 acres (350 km) of riverside floodplain undergoing active restoration.

Restoration projects have re-mobilized some of the sediments that had been trapped behind bank stabilization structures, prompting concerns of exacerbated nutrient and sediment pollution locally and downstream in the northern Gulf of Mexico. A 2010 National Research Council report assessed the roles of sediment in the Missouri River, evaluating current habitat restoration strategies and alternative ways to manage sediment. The report found that a better understanding of sediment processes in the Missouri River, including the creation of a "sediment budget" – an accounting of sediment transport, erosion, and deposition volumes for the length of the Missouri River – would provide a foundation for projects to improve water quality standards and protect endangered species.
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