A peninsula, probably formed by a moraine and subsequently modified by wind-driven accumulation of sand, separates the lake into a north-northwesterly and a south-southeasterly half with different colour and water composition.

The lake is of tectonic origin and lies within a basin bordered by mountain ranges to the east and the west and two volcanoes north and south.

[8] The lake is subdivided into a northern or northwestern and a southern or southeastern part by a[9][1] 20 metres (66 ft) high peninsula, on which wave action has led to the formation of sand spits.

[7] The Astaburuaga River enters the lake on its eastern shore;[12] it originates on the mountains east of Laguna del Negro Francisco where it is nourished by snowmelt.

[17] The watershed of Laguna del Negro Francisco covers a surface area of 930 square kilometres (360 sq mi).

[15][2] The mean discharge of the Astaburuaga is about 0.888 cubic metres per second (31.4 cu ft/s),[18] but it varies strongly over time, including at different hours of the day as the water of the river freezes and remelts.

[19] In addition, some water from the Astaburuaga River flows into the Cíenaga Redonda basin rather than Laguna del Negro Francisco;[18] presently, an alluvial cone separates the Astaburuaga River in the Valle Ancho gorge from the Salar de Maricunga/[20] Cíenaga Redonda watershed.

[6] Geologically, the lake is located in a 200 square kilometres (77 sq mi)[2] north-south trending depression between the Andes in the east and the Cordillera Domeyko in the west;[22] subduction of the Nazca Plate beneath South America is responsible for the formation of these mountain ranges.

[23] On these sides normal faults border the depression which is closed to the north and the south by the Quaternary volcanoes Copiapó and Jotabeche, respectively.

[22] This event is responsible for the formation of Laguna del Negro Francisco within the basin, as without the Astaburuaga's input there would not be enough water to sustain a permanent lake.

During this wet period, glaciers in the region expanded due to the increased availability of moisture and peat bogs formed in valleys.

[36] In prehistory, first pre-ceramic hunter-gatherers and later ceramics-using people who also engaged in horticulture were active in the area of the Astaburuaga River and the Laguna del Negro Francisco.