During the late Pleistocene, Salar de Pajonales formed an actual lake that has left shoreline features.

The extreme environmental conditions have drawn comparisons to Mars, and Salar de Pajonales has been used as an analogue for Martian environments.

The salar lies at the margin of the hyperarid Atacama Desert,[2] on the Altiplano-Puna high plateau[3] at 3,537 metres (11,604 ft) elevation.

[15] A raised area at the eastern end of the salar features small holes draped in gypsum[16] that appear to be produced by degassing.

[21] Salt deposition is influenced by the activity of cyanobacteria and sulfur-oxidizing bacteria,[22] which precipitate gypsum that may entomb microorganisms.

[12] Its catchment covers an area of 1,984 square kilometres (766 sq mi),[1] but lacks permanent surface drainages.

[25] The Lazufre uplift, an area where the ground is rising, lies in close proximity to Salar de Pajonales.

[26] Around the last glacial maximum, water levels in Salar de Pajonales rose by about 50 metres (160 ft), covering an area of about 205 square kilometres (79 sq mi).

[25] The vegetation of the area consists of matorral formed by Fabiana bryoides and Phacelia pinnatifida[34] and steppe dominated by Stipa frigida.