Cly Butte is situated three miles (4.8 km) southeast of the Monument Valley visitor center on Navajo Nation land.

Precipitation runoff from this butte's slopes drains to Gypsum Creek which is a tributary of the San Juan River.

Topographic relief is significant as the summit rises 600 feet (183 meters) above the surrounding terrain in 0.1 mile (0.16 km).

The bottom layer is slope-forming Organ Rock Shale and the upper stratum is cliff-forming De Chelly Sandstone.

The buttes and mesas of Monument Valley are the result of the Organ Rock Shale being more easily eroded than the overlaying sandstone.