2 stretches of the Missouri River are protected here. The portion originally set aside, from Gavins Point Dam near Yankton, South Dakota, to Ponca, Nebraska, still exhibits the river's dynamic character in its islands, bars, chutes, and snags. The second portion includes the land located adjacent to the free-flowing segment between Lewis and Clark Lake and Lake Francis Case. This section represents one of the best natural landscapes associated with the river along its entire course. Native floodplain forest, tallgrass and mixed grass prairies, and the river provide habitats for several endangered bird and fish species. You may fish, hunt, and boat.

The park also includes a 76-mile reach of the Niobrara River, showcasing a stellar example of a Great Plains river and preserving a unique ecological crossroads where 6 distinct ecosystems, some at or beyond their normal geographic limit, mix. The western third of the Scenic River is home to some 90 waterfalls, highest among them topple more than 75 feet to the valley floor. The Niobrara Valley is also a remarkable cultural landscape, famous for its documented fossil sites, dotted with historic resources and small ranches and farms that have been locally owned for generations.