Chacoan flora typifies that of North American high deserts: sagebrush and several species of cactus are interspersed with dry scrub forests of piñon and juniper, the latter primarily on the mesa tops. The canyon is far drier than other parts of New Mexico located at similar latitudes and elevations, and it lacks the temperate coniferous forests plentiful to the east. The prevailing sparseness of plants and wildlife was echoed in ancient times, when overpopulation, expanding cultivation, overhunting, habitat destruction, and drought may have led the Chacoans to strip the canyon of wild plants and game. It has been suggested that even during wet periods the canyon was able to sustain only 2,000 people.
Among Chacoan mammals are the plentiful coyote (Canis latrans); mule deer, elk, and pronghorn also live within the canyon, though they are rarely encountered by visitors. Important smaller carnivores include bobcats, badgers, foxes, and two species of skunk. The park hosts abundant populations of rodents, including several prairie dog towns. Small colonies of bats, are present during the summer. The local shortage of water means that relatively few bird species are present; these include roadrunners, large hawks (such as Cooper's hawks and American kestrels), owls, vultures, and ravens, though they are less abundant in the canyon than in the wetter mountain ranges to the east. Sizeable populations of smaller birds, including warblers, sparrows, and house finches, are also common. Three species ofhummingbirds are present: one is the tiny but highly pugnacious rufous hummingbird, which compete intensely with the more mild-tempered black-chinned hummingbirds for breeding habitat in shrubs or trees located near water. Western (prairie) rattlesnakes are occasionally seen in the backcountry, though various lizards and skinks are far more abundant.