Thunderbird Mesa is situated four miles (6.4 km) southeast of the Monument Valley visitor center on Navajo Nation land.

Precipitation runoff from this mesa'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 rock ranges in age from Permian at the bottom to Triassic at the top, with a major unconformity between the sandstone and Moenkopi.

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