[3] Precipitation runoff from the mountain's slopes drains north into Red Rock Wash and south into Oak Creek.

Topographic relief is significant as the summit rises 2,500 feet (762 meters) above Oak Creek Canyon in less than one-half mile (0.8 km).

Rainbow Mountain is composed of Aztec Sandstone which formed about 180–190 million years ago as lithified sand dunes in a desert during the Early Jurassic.

[5] The red, orange, and brown coloring of the sandstone is caused by the presence of iron oxide or hematite.

Red spots in the buff sandstone are iron oxide concretions called "Moqui marbles."