Cotacotani Lake's main feature is the considerable number of islands and islets that it holds, which are really lava hummocks generated by a past volcanic event.

With a surface of 6 km2, the Cotacotani holds a volume of water between 30 and 40 million of m³, which empty through Lauca River into Coipasa Lake, in Bolivia.

Although much of its present hummocky topography is related to a large volcanic debris avalanche occurred in the zone, this lacustrine area was not originated by such event.

[6] The lake is technically a compound structure consisting of many disconnected water bodies with an average surface elevation of 4,526 metres (14,849 ft) between rocky blocks of andesite and rhyolite that were formed by the Parinacota huge landslide.

[10] Precipitation at Lake Chungara close to Cotacotani is about 331 millimetres per year (13.0 in/year) owing to the effects of the Southeast Pacific High and the rain shadow of the Andes and occurs mainly during December–March in the so-called "Bolivian Winter" when Atlantic moisture arrives.