The lake is less than 2 metres (6 ft 7 in) deep and forms a rough rectangle with a surface of 8.6 square kilometres (3.3 sq mi).

Laguna Negra loses its water through evaporation, and is replenished through surface runoff and groundwater which ultimately originate to a large part from snowmelt.

[8] A prominent alluvial fan borders Laguna Negra to the southeast[6] and its northward growth has generated a shallow water area at the southeastern margin of the lake (Stromatolite Belt).

[19] Lava flows from surrounding volcanoes have closed off the southern outlet of the valley occupied by the lakes.

[2] The lakes lie in the southernmost Puna, a high plateau at an elevation of 3,700 metres (12,100 ft) where a dry climate and Cenozoic uplift generated the Laguna Verde Saline Complex[1] when block faulting generated separated drainage basins[21] separated by north–south trending mountain ranges.

[9] Evidence from other lakes in the region suggests that the environment was wetter than today between about 15,000–14,000 and 13,500–11,300 years before becoming dry during the middle Holocene.

[23] Presently, the climate is dominated by the South Pacific High anticyclone which draws dry air into the region.

During summer, an Atlantic anticyclone conversely transports moister and warmer air to the area, resulting in the formation of convective clouds and precipitation.

[26] In this sector of the Andes, peatlands are the key ecosystems,[22] with the dominant plant species being Distichia muscoides, Oxychloe andina and Plantago rigida as well as graminoids and grasses.

[28] Salt marsh grasses of the genus Spartina grow at the southern end of the lake,[29] and copepods have been observed in ponds;[30] both are linked to areas with lower salinity.

[29] Active tufa formation has been observed, making Laguna Negra one of only two lakes in the region[c] where it takes place.

[8] These microbialites are found mainly in the northeastern Stromatolite Belt, while its central and western portions feature abiotic carbonate precipitation.

[29] Colours range from green-yellow over orange to snow white, and the structures have the appearance of rocks strewn onto and emerging from the shallow lake.

[39] So-called "diatom blooms" are linked to white carbonate precipitates[42] that form bright spots on the coloured mats.

[43] The colours of the microbial constructs are due to carotenoid and scytonemin pigments, which serve to protect the microorganisms from UV radiation.

[46] Precipitation of carbonates is often associated with life and may be induced by the latter for various reasons,[44] although at Laguna Negra it can also occur independently from biological activity.

[44] The microbial mats are found in the less saline sector of Laguna Negra, implying that reduced salt stress favours their development.