The lake lies in a tectonic depression, which is geologically related to the fault system Miscanti-Callejón de Varela; once it was thought that the lake was in a caldera. The Altos de Toro Blanco mountains separate Lejía Lake's drainage basin from the Salar de Aguas Calientes catchment. A lineament known as the Tumisa line runs along the southern shore of the lake, and appears to have been the site of three earthquakes in post-glacial time. The lake is influenced by volcanic activity from the neighbouring Lascar; ash and pyroclastic material entered Lejía Lake in 1993, and the large Soncor eruption from this volcano 26,450 years before present filled the lake.