It runs through a narrow canyon cut into ancient lava flows in southwestern Idaho.

The Bruneau Canyon, which is up to 1,200 feet (370 m) deep and forty miles (65 km) long, features rapids and hot springs, making it a popular whitewater trip.

[2] The Bruneau River system originates within and near the Jarbidge and Mountain City Ranger Districts of the Humboldt–Toiyabe National Forest in northern Elko County.

This lower section of the watershed is occupied by farms and ranches, and the town of Bruneau.

Irrigation withdrawals result in a number of its tributary streams being largely dewatered annually.