This study examines the limnology and ecology of two high altitude wetlands, Lirima (19°51’24 S; 68°55’02 W; 4000 m asl) and Caya (20°37’21 S; 68°58’28 W; 3700 m asl), located in the Chilean Altiplano. Both wetlands are formed by the evaporitic remnant basins of paleolakes which occupied an extensive area of what today is known as the Altiplano. These systems have a negative hydrological balance, receiving their water from groundwater, snow melt and limited seasonal rains. An ongoing negative water balance and the sediment characteristics in the region have accelerated the salinization process in these systems, as shown by their present physicochemical characteristics. Nutrient values were typical of mesotrophic to eutrophic systems. The ionic content classifies Lirima as a sodium sulfated wetland and Caya as a calcium chloride one. Conductivity values ranged between 778 μS/cm at Lirima to 2100 μS/cm at Caya, and were reflected in the differences in biodiversity found in these systems. The Lirima wetland supports a population of the endemic fish Orestias aff. agassii found in several Evolutionary Significant Units (ESU) across the region. Microbial diversity in the water column was characterized by the presence of 5 bacterial phyla and related genera (e.g. Psychrobacter, Bacillus, Eryhtobacter, Halomonas). We present information on several key ecosystem components including macrophytes, plankton, benthos, fish and birds. This descriptive paper highlights the unusual limnological and biological characteristics of high altitude wetlands and highlights the importance of describing their biological communities across levels of organisation (e.g. microbial through to higher vertebrates) as well as their functional role, interactions and sensitivity to changes in water availability.