The designation was first applied in 1978 to a 59-mile section of the Missouri River between Gavins Point Dam and Ponca State Park.

The Yellow Stone was the first steamboat to sail this stretch of the river in 1832 on the way to Fort Union Trading Post.

The Flood Control Act of 1944 (the Pick–Sloan Plan) created the Fort Randall and Gavins Point dams, causing major changes to the river's hydrology and habitats.

[2] New deposits such as sandbars and accretions adjacent to the riverbanks are covered with the pioneer species: annual weeds, short-lived grasses, sedges, and seedling willow and cottonwood.

The sparse vegetation under the mature cottonwoods consists mostly of scouring rush, Kentucky bluegrass, smooth brome, and other invasive grasses and weeds.

Since the days of Lewis and Clark the larger mammals have disappeared, including the grizzly bear, bison, and elk.

Small mammals, including mice, voles, bats, rats, and ground squirrels make up the bulk of the species within the park.

Fish and Wildlife Service to help manage habitat for threatened and endangered species, especially the Piping plover, Least tern, and Pallid sturgeon.

Often during the summer months sandbars are signed as "Closed" to help protect critical habitat, fines and other penalties can be imposed for violators.