The Wenaha and its tributaries form an extensive network of steep canyons sliced into volcanic rock layers of the Columbia River basalts, which covered the region during massive eruptions millions of years ago.

Once used by four Native American tribes for hunting, fishing and trade, the Wenaha River basin was surrendered by the Nez Perce to the US government in the 1860s.

The few settlers that subsequently came to this rugged, inaccessible region used it primarily for livestock grazing, causing severe damage to the local grasslands and soils.

[7] The 13.8-mile (22.2 km) long[8] North Fork Wenaha River originates near Ski Bluewood to the east of Deadman Peak in Columbia County, Washington, at an elevation of 5,885 feet (1,794 m),[9][n 1] and flows south into Oregon.

[7][10][11] The 12.2-mile (19.6 km) long[8] South Fork Wenaha River begins in the southwest corner of Wallowa County, at an elevation of 5,723 feet (1,744 m),[12][n 2] and flows northeast to the confluence.

[7][13] From the forks, the Wenaha River flows east, cutting a deep canyon through rugged plateau country on the eastern flank of the northern Blue Mountains.

The area experiences cold, snowy winters between November and April with snowpack building as much as 5 feet (1.5 m) deep at higher elevations.

[3] The basin provides habitat for numerous animal species include Rocky Mountain elk, white-tailed deer, moose, black bear, gray wolf, coyote, cougar, bobcat, snowshoe hare, and bighorn sheep.

[citation needed] Explorers' and pioneers' accounts starting in the 1860s noted that the elk population was rich to the south of the Wenaha River and across most of what is now the Wallowa-Whitman National Forest.

[22] The Grouse Flats wolf pack, which had about nine adults in 2022, has been observed primarily on the north side of the Wenaha River with most of its range in Washington.

[23] The Grouse Flats pack has been implicated in a number of livestock killings and the Washington Department of Fish and Wildlife authorized lethal removel of some wolves in 2019.

[24] The Wenaha River is considered a Type IV channel under the Rosgen Stream Classification, characterized by a shallow rocky bed interspersed with deep pools.

[3] Although the river flows through a rugged, mountainous region, its gradient is relatively low at 1.1 percent, and is bordered by floodplains with dense riparian hardwood forests along its valley floor.

[29]: 7–14  Populations have remained low and unstable since then; the average chinook salmon return for the period 1995–2005 was 376 fish, not counting those of hatchery stock.

These flows blocked westward drainage from the Troy basin, and in their aftermath a landscape of lakes and peat bogs formed in the area, later to be buried by fluvial sandstones and siltstones.

The modern Wenaha and Grande Ronde channels began to take shape and cut down into the basalt layers, eventually forming a massive system of canyons.

[30] The Wenaha River channel developed along the axis of the Grouse Flat syncline, a geologic fold that formed with the Blue Mountains uplift.

On September 13, after traveling over 20 miles (32 km) across a dry, rugged landscape, they reached the upper Wenaha, likely becoming the first Europeans to see the river.

They camped near the river's confluence with Butte Creek and the following day they traveled down the Wenaha to the Grande Ronde, where they traded horses with the natives.

In 1855 the Nez Perce, under pressure from the influx of white settlers, surrendered 7.5 million acres (30,000 km2) in exchange for monetary compensation and infrastructure development.

[citation needed] Access to this area was initially difficult and all supplies were moved by pack horses over steep mountain trails.

In 1902 the first store was established in Troy, and in 1912 a flour mill was built on the Wenaha River, followed by a post office, hotel, school and other buildings.

[21] The first cattle drive to Grouse Flats was attempted in the spring of 1887 and met numerous challenges, including deep snow and thunderstorms, on the way from Pomeroy, Washington.

Schmitz, the first forest supervisor, found that "the main reason for the overgrazing of the interior was that each spring long before the range was fit to graze there would be a race to get the sheep over the divide and located on the best camps.

[21] Many of the present day hiking trails along the Wenaha River and its tributaries were also built during this time, along with nearby fire lookout towers, corrals, and other forest infrastructure.

[3] In the mid-1970s, the Forest Service proposed salvage logging 30,000 acres (12,000 ha) above the South Fork after a tussock moth infestation caused severe tree mortality.

A final 0.15 miles (0.24 km) between the Wenaha State Wildlife Area and the confluence with the Grande Ronde River are designated as Recreational.

[50] With access limited to those on foot or horseback, the Wenaha River country remains lightly used and provides numerous backcountry recreation opportunities.

[52] The Wenaha Wildlife Area near Troy is open to upland bird hunting for grouse, chukar, wild turkey and waterfowl.

[53][54] The Wenaha River Trail follows the main stem and south fork for 31 miles (50 km), starting at Troy and heading west to Timothy Springs trailhead, more than 3,000 feet (910 m) higher in elevation.