Aravaipa Canyon Wilderness is in the Basin and Range province and is surrounded by two mountain ranges, the Galiuro and Santa Teresa mountains. The Galiuros are mainly a thick pile of Tertiary volcanic rocks and the Santa Teresas consists mostly of Tertiary granite. This geological diversity was of interest to miners. Many abandoned lead, zinc and copper mines exist throughout the region.

The cavernous, buff-and-brown colored walls you see as you walk through the canyon from the east are composed of Hell Hole Conglomerate, which extends to Parson's Canyon on the south wall and Hell Hole Canyon on the north wall. From here and continuing west, the Galiuro Volcanics begin and shape Paisano Canyon, and from Booger to Horse Camp Canyon. This mid-portion of the canyon displays impressive red, orange, and gray walls with columns towering over 1,000 feet.

On the West end of the canyon, between Virgus and Hell's Half Acre canyons, the creek cuts through a dark red porphyry (rock containing crystal structures). This rock is considered part of the Pinal Schist group which originated in the Precambrian Era. It is older and harder that the other formations and may be why the stream has cut a narrower channel in this area.