Although Tonto National Monument was established to preserve the cliff dwellings, it also protects a great diversity of plants and animals. The Monument covers less than two square miles in area, but is home to at least 160 species of birds, 6 species of amphibians, 32 species of reptiles, 26 species of land mammals, and at least 14 species of bats.

The Monument's great diversity can be explained in part by its location on the edge of two very different landforms: the Superstition Mountains to the southwest, and the valley formed by the Salt River and Tonto Creek to the north and east. Between valley and mountains lies an apron, or bajada, of eroded sediments, bisected by dry washes. As the bajada slopes north towards the river (now Roosevelt Lake), conditions become drier and warmer, and the vegetation is more open and desert-like. Not surprisingly, the short distance from the mountains to the valley brings many changes in wildlife.

One other feature of great significance to animals is Cave Creek Canyon, which runs below the Upper Cliff Dwelling, through the Visitor Center area, and north to Roosevelt Lake. North of the Visitor Center, Cave Creek Canyon is dry for most of the year. To the south, however, it contains a perennial spring and tall trees, including Arizona walnuts and sycamores. This small shaded riparian area is visited by many species of wildlife, and was no doubt heavily used by the Salado, who built their dwellings overlooking the spring.

A study of the wildlife was conducted from 1993 - 1995 by biologists from the University of Arizona. Click on the link for an animal list.