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Natural history

Historically, the thousands of square miles that comprised the floodplain of the Missouri River supported a wide range of plant and animal species. Biodiversity generally increased proceeding downstream from the cold, subalpine headwaters in Montana to the temperate, moist climate of Missouri. Today, the river's riparian zone consists primarily of cottonwoods, willows and sycamores, with several other types of trees such as maple and ash. Average tree height generally increases farther from the riverbanks for a limited distance, as land next to the river is vulnerable to soil erosion during floods. Because of its large sediment concentrations, the Missouri does not support many aquatic invertebrates. However, the basin supports about 300 species of birds and 150 species of fish, some of which are endangered such as the pallid sturgeon. The Missouri's aquatic and riparian habitats also support several species of mammals, such as minks, river otters, beavers, muskrats, and raccoons.

The World Wide Fund For Nature divides the Missouri River watershed into three freshwater ecoregions: the Upper Missouri, Lower Missouri and Central Prairie. The Upper Missouri, roughly encompassing the area within Montana, Wyoming, southern Alberta and Saskatchewan, and North Dakota, comprises mainly semiarid shrub-steppe grasslands with sparse biodiversity because of Ice Age glaciations. There are no known endemic species within the region. Except for the headwaters in the Rockies, there is little precipitation in this part of the watershed. The Middle Missouri ecoregion, extending through Colorado, southwestern Minnesota, northern Kansas, Nebraska, and parts of Wyoming and Iowa, has greater rainfall and is characterized by temperate forests and grasslands. Plant life is more diverse in the Middle Missouri, which is also home to about twice as many animal species. Finally, the Central Prairie ecoregion is situated on the lower part of the Missouri, encompassing all or parts of Missouri, Kansas, Oklahoma and Arkansas. Despite large seasonal temperature fluctuations, this region has the greatest diversity of plants and animals of the three. Thirteen species of crayfish are endemic to the lower Missouri.