The Missouri National Recreational River is a partnership-based park. Within the 126-mile Missouri River corridor the National Park Service works with federal, state, county, and city agencies as well as commercial interests, private citizens and public interest groups.

Among the park's many partners are:

 U.S. Army Corps of Engineers

South Dakota Department of Game, Fish and Parks

Nebraska Game and Parks Commission

MNRR Water Trail

Missouri River Futures

Missouri River Institute at University of South Dakota