The headwaters of the Salmon River are in the Sawtooth National Recreation Area. Multiple BLM recreation sites provide the public river access starting at the East Fork confluence, followed downstream by Deadman Hole, Bayhorse, Challis Bridge and Cottonwood.

The BLM-managed section of the upper Salmon River starts along Idaho State Highway 75 and the confluence of Thompson Creek and flows through public and private land over 50 miles to McKim Creek where it enters the BLM Salmon Field Office area.