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The Pueblo Mountains Wilderness Study Area (WSA) is located 96 miles south of Burns and 5 miles south of Fields, Oregon. Almost all of the WSA is within Harney County, although a small portion crosses the state line into Humboldt County, Nevada. The entire WSA lies to the west of the main north-south county road which runs between Fields and Denio, Nevada. The nearest major highway is Nevada State Highway miles to the south of the WSA.

The WSA is an irregularly-shaped area containing 68,710 acres of Bureau of Land Management (BLM) land in Oregon, plus 600 acres of BLM land in Nevada. In addition, there are 3,380 acres of split-estate lands in Oregon.

At the extremes, the WSA is 15 miles long and 11 miles wide. The boundary is formed by a combination of private land, BLM roads, a paved county road (east side only), and legal subdivisions. In addition, 12 low standard dead end dirt roads (totaling 17 miles) enter the WSA from various points around the perimeter and also form part of the boundary. One of the roads ends at a 320 acre parcel of private property, making the parcel a part of the boundary even though it is surrounded by the WSA.

The most prominent physical feature of the WSA is the Pueblo Mountains ridgeline which runs north and south along the entire length of the western half of the WSA. This is a tilted fault block mountain range, the eastern side of which has been uplifted along a north-south trending fault. Averaging 7,300 feet in elevation along the crest, the eastern face of this ridge is steep, rugged, and rocky while much of the western slope is like a table top tilted to the west at nearly a 20-25 degree angle.

Less than 3 miles east of the western ridge lies a shorter (g-mile-long) north-south ridgeline. Along this ridgeline is Pueblo Mountain. At 8,634 feet, it is the second highest peak in southeastern Oregon and the highest point in the WSA. Two major drainages originating in the central portion of the WSA, Willow Creek and Cottonwood Creek skirt this ridgeline to the north while both Arizona Creek and Van Horn Creek cut through the ridge within rugged canyons. Denio Creek also cuts through the ridge; a portion of this drainage is outside the WSA to the south.

Although steep, the east slope of the eastern ridge is much less rugged and rocky than the east slope of the western ridge. The eastern ridge gives way to foothills and lowlands along the eastern boundary as it merges with Pueblo Valley.

It is along the eastern boundary that the WSA reaches its lowest elevation (at several points) of just under 4,200 feet. A series of valleys, basins, and meadows lie in the erosional valley between the two ridges.

The WSA was initially studied under Section 603 and 202 of the Federal Land Policy and Management Act (FLPMA). Lands added after the wilderness inventory were studied under Section 202, also of FLPMA. These lands were included in the final Oregon Wilderness Environmental Impact Statement filed in February of 1990.