Native, pre-settlement vegetation consisted primarily of shrubs, perennial bunchgrass, a variety of forbs and a living soil crust composed of lichens, moss and algae. The state of Washington has designated shrub-steppe communities as a priority habitat because of their significance to a number of wildlife species and the scarcity of this habitat type. In addition, the U.S. Department of the Interior (DOI) has identified native shrub and grassland steppe in Washington and Oregon as an endangered ecosystem.
The Monument blends a desert environment with one of the largest river complexes in the country, providing an exceptionally wide variety of habitats within a relatively small assemblage of public lands. Each of these two sharply contrasting environments—desert and river—has its own diverse wildlife populations. The Monument also offers other habitat types. The White Bluffs provide cliff surfaces. Wetlands, some natural, some not, offer water in an otherwise arid environment. Rattlesnake Mountain is tall enough to offer a lithosol environment. Microbiotic crust is one of the smallest "micro-habitats" found anywhere and is critical for the larger shrub-steppe habitat. The shrub-steppe itself is comprised of two different habitat types—the "steppe" habitat supporting those species needing grass to survive and the "shrub" component, which are the "trees" and overstory of the Monument.
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Once a national wildlife refuge itself, Saddle Mountain National Wildlife Refuge still exists, but as part of the much larger Hanford Reach National Monument.