Several "outstandingly remarkable values" have been designated to be protected along the Niobrara National Scenic River, including: Fish and Wildlife, Scenery, Fossil Resources, Geology, and Recreation.

The westernmost 26 miles (40 km) of the Scenic River section, from the Fort Niobrara National Wildlife Refuge (just east of Valentine) to the Rocky Ford portage, offer canoeing, kayaking, and tubing opportunities.

Considered an extraordinary example of a Great Plains river, the Niobrara is home to over 500 plant species many at or beyond their usual range, including many not otherwise naturally found within several hundred miles.

Northern boreal forest types occur on north facing slopes where shade and abundant ground water create cooler microclimates.

Larger fish, such as rainbow and brown trout, prefer cooler, clear water where springbranch canyon tributaries enter the river.