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Abstract Background Knowledge of immature habitats is an important focus for investigations of mosquito community ecology, and may improve our understanding of how environmental variables increase risk of mosquito-borne diseases by influencing the distributions and abundances of species. In Patagonia region, where climatic and ecological factors could be only borderline suitable for mosquito development, relatively little is known about larval ecology. The present study focuses on associations of environmental conditions in natural aquatic habitats with abundances of mosquito species that have colonized such habitats in Patagonia. Methods We described the mosquito community composition within 26 natural temporary pools, and assessed the general relationships between environmental variables (pH, water temperature, conductivity, salinity, dissolved oxygen, aquatic plant cover and main nutrients) and larval abundances using redundancy analysis (RDA). Additionally, we compiled monthly climate data and vegetation indices for each larval habitat, and estimated the probability of presence for two of the most abundant species, describing through generalized linear models (GLM) the environmental, climatic and landscape variables-probability of occurrence relationships. Results Seven species belonging to the genera Culex and Aedes were identified, with Culex apicinus, Cx. acharistus and Aedes albifasciatus being the most abundant. Mean larval densities were low (6.8 ± 2.8 larvae/dip), and the highest species richness and larval densities were recorded in northern and central areas. Aedes albifasciatus, a species of sanitary importance, was widely distributed, being the only one collected south of the 45th parallel of S latitude. RDA indicated that aquatic conductivity, pH, water depth, dissolved oxygen, ammonia and soluble reactive phosphorous accounted for the main part of the variation in the species composition. According to GLMs, wind speed was the variable that best described the presence of Ae. albifasciatus, and the probability of finding this species was positively associated with high wind speed values. On the other hand, the EVI vegetation index was the only variable included in the Cx. apicinus model, whereby there was a great probability of presence in arid areas with lower EVI values. Conclusions Our results enhance our knowledge of larval habitat ecology under the extreme environmental conditions of Patagonia and will guide future efforts to understand how multiple effects can affect mosquito ecology and public health at higher latitudes.