San Pedro de Atacama is located in the watershed of the Atacama Salt Flat, in the andean zone of the Atacama desert, the driest desert in the world. It is surrounded by three mountain ranges, which stop humid winds from entering the sector.

To the east there is the Andes Mountain Range, formed by a vast quantity of volcanoes towering up to 5,000 m (16,404 ft) above sea level. Volcanoes such as Licancabur, Lascar, Sairecabur and Putana are prominent in the area, provoking volcanic activity which reflects in geysers and thermal pools. At around 4,000 m (13,123 ft) high there is a plateau known as Altiplano or High Plateau, with small lakes and wetlands.

To the west there is the Domeyko Mountain range, at an average altitude of 3,300 m (10,827 ft), featuring the Quimal mountain at 4,300 m (14,108 ft). On this side there is also the Salt Mountain Range (2,300 mts or 7,547 ft) formed by folds in the earth's crust and shaped by wind and water erosion.

To the south there is the Atacama salt flat, the greatest saline deposit in Chile, holding 40% of the world's reserve of Lithium. This salt flat is a large lagoon of salt water, formed by rainwater from the high plateau and high mountain that are unable to pass the barrier of the Domeyko mountain range and stagnate in this watershed forming a white and rough crust of salt and other sediments from the surrounding mountains and that are transported by water and wind.