Flowing generally east near the headwaters and then north through Wallowa County, the entire river is designated Wild and Scenic.

[8] It follows a geologic fault to the Snake River, and in addition to land in the Wallowa–Whitman National Forest and private land, its corridor includes parts of three special management areas: the Eagle Cap Wilderness, Hells Canyon National Recreation Area, and Hells Canyon Scenic Byway.

[9] Formed by the confluence of its north and south forks, the Imnaha River begins at Cusick Mountain and the western slope of Mount Nebo in the Eagle Cap Wilderness and the Wallowa–Whitman National Forest.

It flows east and then north and north-northeast along the Imnaha Divide through Wallowa County, Oregon, for about 64 miles (103 km) to the Snake River on the Oregon-Idaho border.

Near the confluence with Dry Creek, the river passes under the Hells Canyon Scenic Byway, also known as the Wallowa Mountain Loop and as NFD 39.

About 1 1/4 miles below Gumboot Creek is the Imnaha River Acclimation Site and Weir, where adult Chinook salmon are collected and smolts are released for the hatchery supplementation program.

Soon Neil Canyon and Johnson Creek, where Upper Imnaha Road crosses to the left bank, enter from the right.

[9][10] Below the historic forest ranger station, Adams, Schleur, Spring, Snell, Loyd, Keeler, Jody, Thorn, Dunlap, Rippleton, Dead Horse, High Camp, and Deer creeks enter from the right before Sheep Creek enters from the left near Imnaha at RM 19.5 (RK 31.4).