During glacial times, the lake was considerably larger owing to decreased evaporation and increased precipitation rates, with bioherms developing around the waterbody.

[4] The city of San Pedro de Atacama lies 103 kilometres (64 mi) northwest of Lejía Lake.

[5] The lake basin is surrounded by volcanoes, such as Aguas Calientes, Lascar, Tumisa, Lejía, Chiliques and Cordon de Puntas Negras,[5] and smaller centres like Cerro Overo and La Albòndiga.

[6] The lake is endorheic and has a 193 square kilometres (75 sq mi) large catchment,[5] and a lava flow forms its southern shore.

[15] Sulfate and sodium are the principal salts in the lake water, with chloride and magnesium secondary and calcium, potassium, silica and strontium subordinate.

[16] The lake is nourished from the north through two creeks, one originates on Aguas Calientes and the other from two tributaries on Lascar and Cerro del Abra.

[8] A groundwater outlet appears to exist, considering that there is no halite accumulating in the lake,[17] and Cerro Overo is a maar that formed through groundwater-magma interaction.

[5] A lineament known as the Tumisa line runs along the southern shore of the lake,[7] and appears to have been the site of three earthquakes in post-glacial time.

[32] The ecosystem of Laguna Lejía is exposed to high UV radiation, intense day-night temperature cycles, and lack of water.

[36] Shoreline vegetation consists of Calandrinia, Deyeuxia, Puccinellia and Stipa species, which occur close to waterbodies and springs.