The most abundant mammal of shrub-steppe habitat of the Monument is the Great Basin pocket mouse (Perognathus parvus). The deer mouse (Peromyscus maniculatus), western harvest mouse (Reithrodontomys megalotis), northern grasshopper mouse (Onychomys leucogaster), bushytail woodrat (Neotoma cinerea), and northern pocket gopher (Thomomys talpoides) are other common small mammals using habitats on the Arid Lands Ecology Reserve (ALE). Least chipmunks (Eutamius minimus) are found in the upper elevations of Rattlesnake Mountain, and sagebrush voles are relatively common above 1,000 feet (305 m) elevation in sagebrush habitat.
Porcupines (Erethizon dorsatum) are typically restricted to riparian areas where they feed on the bark of small limbs and tree branches. Black-tailed jackrabbits (Lepus californicus) are usually common in mature sagebrush habitat. White-tailed jackrabbits (L. townsendi) occur in sagebrush/bunchgrass habitats, generally at higher elevations than black-tailed jackrabbits. The populations of both species are cyclical and are currently at low levels throughout the Columbia Basin.
Large mammals found on the ALE include the occasional cougar (Felis concolor), bobcat (Felis rufus), and badger (Taxidea taxus). These species are present throughout the Hanford Site in low numbers. A resident elk (Cervus elaphus) herd uses the ALE site portion of the National Monument. Mule deer (Odocoileus hemionus) densities on the ALE and along the Columbia River are the highest among Hanford habitats. Coyotes (Canis latrans) are the most abundant large carnivore on the Monument.
The lack of sufficient roost habitat probably limits the density and diversity of bats on the Monument. Bats may be more common in areas adjacent to the Columbia River and in riparian zones around desert springs and lakes created by irrigation return. Studies in the general Hanford vicinity have documented the presence of pallid bat (Antrozous pallidus), silver-haired bat (Lasionycteris noctivangans), and western small-footed myotis (Myotis ciliolabrum). The extent to which these species use the Monument is not known.