Its flat top is part of a stack of multiple 80 mi (130 km)-long lava flows that have been eroded to form a series of mesas that extend from Knights Ferry to Sonora, California.

Further north and closer to their source areas, the Mehrten and Valley Springs formations consist of volcanic and volcanoclastic deposits that have been divided into several stratigraphic units, e.g. the Relief Peak Formation, Stanislaus Group, etc., based on their age and source volcanic center.

[4][5] Lying buried beneath the volcanoclastic sediments of the Mehrten and Valley Springs formations within the Table Mountain region are paleovalleys cut into pre-Cenozoic bedrock.

[4][5] By 1911, Lindgren[7] had largely reconstructed the courses of these ancient river valleys and systems cut into basement rocks and filled with the gold-bearing Auriferous gravels.

As a result, the prevolcanic unconformity lying at the base of the Mehrten and Valley Springs formations has been exhumed and is now exposed as the modern rolling topography adjacent to Table Mountain.

In the spring, many wildflowers can be found atop the mountain including several species of lupine and the yellow mariposa lily, Calochortus luteus.

[9] Vernal pools form on the flat top after heavy winter and spring rains, providing habitat for many uncommon plant and animal species.