It serves as a magnet for a wide diversity of wildlife species and is strategically located along migration corridors serving both the Pacific and Central Flyways. The refuge has been identified as one of 500 Globally Important Bird Areas by the American Bird Conservancy.

The National Park Service designated the South Marsh a National Natural Landmark because of the biological diversity and pristine condition of the habitat. The refuge is one of the most important waterfowl nesting areas in the Great Basin and intermountain West.

The South Marsh supports the largest population of nesting canvasback ducks west of the Mississippi River (outside Alaska), and holds the highest concentration of nesting canvasbacks in North America. Due to habitat loss elsewhere in the Great Basin, the refuge has become increasingly important to resident wildlife, including mule deer, pronghorn antelope, and sage grouse. The refuge fishery is popular with local anglers.

It is not passable in winter and is never recommended for large trailers or motor homes. Alternate routes, open all year, include U.S. Highway 93 south of Wells to State Highway 229 and County Road 767 (improved gravel), a total of 80 miles; or Interstate 80 at exit 321 through Secret Pass to County Road 767, a total of 90 miles from Elko. A calling card phone is located at Ruby Lake Resort (10 miles north of refuge headquarters).

Fuel and basic groceries are not always available in Ruby Valley; and there are no sales outlets for State hunting and fishing licenses. Contact the refuge headquarters for current information.

These habitats are critical to the existence of many species of wildlife because wetlands are rare in the Great Basin high desert. The islands and bulrush provide nesting sites for waterfowl, marsh bird, and songbird species. Submerged marsh plants growing in open water areas provide feeding sites for birds. Water elevations in some marsh units are controlled to provide nesting and feeding areas for waterfowl and other marsh birds.

Vegetation in the meadows and grasslands is managed to provide nesting cover and feeding areas for wildlife. Transition areas between marsh and upland habitats are dominated by sedges, rushes, grasses, and forbs. Meadows and grasslands are important to migratory birds for feeding and nesting. Grasslands, which contain a different complex of vegetation than meadows because grassland soils are drier, provide nesting cover for waterfowl and songbirds.

These areas also support large populations of small mammals, which are an important food source for birds of prey. Over time, vegetation in meadows and grasslands becomes heavily matted and nesting habitat is lost. Prescribed fire is used to remove matted vegetation, restoring nesting habitat. Cattle grazing and haying are used as habitat management tools to provide feeding areas for birds.

Shrub-steppe upland habitat dominates the dryer sites on the refuge. Sagebrush is the principal shrub species on the west side of the marsh, and greasewood dominates the east side. Great Basin wild rye, a prevalent grass species, is abundant in the shrub-steppe and grassland plant communities. Migratory and resident bird species use shrub-steppe areas for feeding and nesting.