Resident mammals include mule deer, white-tailed deer, beaver, muskrat, badger, bobcat, coyote, striped skunk, raccoon, porcupine, long-tailed weasel, black-tailed prairie dog, black-tailed jackrabbit, desert cottontail, at least six species of bats, and a wide variety of rodents that are typical of the area grasslands.  Other mammals that have been documented on the refuge include pronghorn, elk, mountain lion, black bear, and ring-tail cat.  

Surveys on the refuge have documented 14 reptile species; including common lesser earless lizard, prairie lizard, pygmy short-horned lizard, common checkered whiptail, Great Plains skink, and snapping turtle.  When the weather turns warm a visitor might see one of eight identified snakes on the refuge; including cornsnake, plains hog-nosed snake, western coachwhip, bullsnake, plains gartersnake, terrestrial gartersnake, western diamond-backed rattlesnake, and the prairie rattlesnake.

The nine amphibians on the refuge include the tiger salamander, American bullfrog, northern leopard frog, boreal chorus frog, Great Plains toad, red-spotted toad, Woodhouse’s toad, western spadefoot, and the plains spadefoot.

Lake 13 is stocked annually by the New Mexico Department of Game and Fish with rainbow trout and channel catfish.  Yellow perch, black bullhead, green sunfish, bluegill, walleye, northern pike, and largemouth bass are all found in refuge lakes.  More elusive fish in the lakes are white sucker, plains killifish, and fathead Minnow.

Common aquatic invertebrates on the refuge include damselflies and dragonflies, mosquitoes and midges, mayflies, diving beetles, water fleas, crayfish, snails and backswimmers.  Terrestrial invertebrates known to occur on the refuge include beetles, true bugs and kin, wasps and bees, grasshoppers, moths and butterflies, and spiders.