Agricultural and residential development, as well as recreational activity, has altered the wildlife community of the Monument. Mule deer are common. Red foxes, coyotes, badgers, cottontail rabbits, and yellow-bellied marmots are upland residents. River otter, beaver, muskrat, mink, and other furbearers are found in and around Hagerman’s ponds, marshes, and waterways.
The most visible species, when its population is high, is the black-tail jackrabbit. Cottontail and pygmy rabbits are also present. Other species include Townsend's and Richardson's ground squirrels (Spermophilus spp.), canyon mouse (Peromyscus spp.), wood rats (Neotoma spp.), marmots or rockchucks (Marmota flavivventris), and kangaroo rats (Dipodomys ordii).
Predators include coyotes (Canis latrans), badgers (Taxidea taxus), spotted skunks (Spilogale putorius), striped skunks (Mephitis mephitis), weasels and mink (Mustela spp.), and an occasional bobcat (Lynx rufus).