 Many U.S. national parks , such as Glacier National Park , Rocky Mountain National Park , Yellowstone National Park and <unk> National Park are in the watershed . Parts of other rivers in the basin are set aside for preservation and recreational use – notably the Niobrara National Scenic River , which is a 76 @-@ mile ( 122 km ) protected stretch of the Niobrara River , one of the Missouri 's longest tributaries . The Missouri flows through or past many National Historic Landmarks , which include Three Forks of the Missouri , Fort Benton , Montana , Big Hidatsa Village Site , Fort Atkinson , Nebraska and Arrow Rock Historic District . 
