During its highstands it covered an area of 1,200 square kilometres (460 sq mi) with a maximum depth of 70 metres (230 ft), and split into several separate lakes while drying out.

The lake last appeared during the last glacial maximum (LGM) and dried out at the beginning of the Holocene, with the last remnant disappearing about 5,000 years ago.

Presently, the Very Large Array radiotelescopes are located on the basin of the former lake, and core samples taken from its bed have been used to reconstruct the past vegetation of New Mexico.

State Road 12 runs along part of its northwestern shore, and U.S. Route 60 crosses over the northeastern lake bed.

[8] Water covered an area of 1,200 square kilometres (460 sq mi) and had a maximum depth of 70 metres (230 ft);[4] the Wisconsin glaciation-age lake reached 2,115 metres (6,939 ft) elevation and had an area of 785 square kilometres (303 sq mi).

[28] The fauna that lived around the lake share characteristics with present-day populations that occur at higher elevations and/or farther north.

[29] Animal fossils found in lake deposits include unidentified species,[30] but also fish and:[31] Based on a 300 metres (980 ft) long core drilled into the floor of the basin, sedimentation goes back to the Pliocene but was variable over time.

[15] During the cold temperatures of the LGM 20,900 years ago, water levels reached 2,110–2,120 metres (6,920–6,960 ft) elevation.

[43] By around 13,200 years ago, water levels had dropped beneath the 2,105 metres (6,906 ft) elevation[44] of the "Bat Cave shoreline".

[45] Subsequent wet periods occurred during the Bolling-Allerod and Younger Dryas,[46] supported by a stronger North American Monsoon.

[49] Presently, there is no permanent water body in the Plains of San Agustín, but ephemeral lakes sometimes form after wet years.

[51] Numerous Paleoindian archeological sites have been found at the former lake, which provided important resources for early humans during the end of the ice age.

Bat Cave faces the southwestern basin[5] and formed through wave-cut erosion by Lake San Agustín.

[25] Various projects to manage the cultural heritage took place in the San Agustín area, of mostly limited spatial extent except for those associated with the Very Large Array.

[71] West of the graben lies the dominating Horse Mountain volcano, which was active 14 million years ago, and there are other volcanic buttes in the vicinity.