The Merced and its South Fork possess outstandingly remarkable scenic, recreational, fish, wildlife, geological, historical/cultural, and ecological values. From its sources in Yosemite Park, the Merced and South Fork Merced flows past exceptional scenery, including glaciated peaks, alpine lakes and meadows, and rugged foothill canyons spangled with spring wildflowers. The river provides a wide variety of recreation in the National Park and along the downstream National Forest and BLM lands. Trails along the South Fork and lower Merced Rivers are particularly popular for their springtime wildflower display. The river supports native wild trout and the only known populations of the limestone salamander. Because much of the river flows through existing wilderness and roadless areas, it possesses a high degree of biotic integrity.
Designation by Congress killed a proposed hydroelectric dam near El Portal. More recently, proponents of a potential raise of New Exchequer Dam on the Merced have pushed legislation in Congress to eliminate about a mile of the lower Merced Wild River to allow for reservoir expansion. But this would flood much of the habitat for the protected limestone salamander and river segment enjoyed by whitewater boaters and hikers in the Merced River Wilderness Study Area.