In 1988, the upper 16 miles (26 km) of the Lostine River were listed as Wild and Scenic.

A 5-mile (8 km) segment in the wilderness below the river's source at Minam Lake were classified "wild".

Irrigation diversions, which play a significant role in the river, contributed to the extinction of the local run of Coho salmon in the 1960s and reduced the population of the run of spring Chinook salmon to a low of 13 fish in 1999.

The Nez Perce began restoration efforts in the 1990s, and by 2005, the Chinook salmon run had risen to 800 fish.

[6] An agreement that year among farmers, the Nez Perce, and the Oregon Water Trust led to efforts to preserve the stream flow during summer, helping the salmon to survive.