The Great Lakes region of western Mongolia includes a diversity of lake ecosystems, from alpine freshwater to lowland, saline lakes, which increasingly face environmental threats from excessive grazing and climate change. We assessed environment-species relationships and patterns of biodiversity of non-biting midges (Diptera: Chironomidae) in 55 western Mongolian lakes using surface-floating pupal exuviae. Overall, the gamma diversity of chironomids from these lakes was high with 117 taxa, but alpha diversity was relatively low. Results from canonical correspondence analysis indicated that chironomid communities were most strongly related to salinity and water temperature. Indicator species analysis identified 12 taxa which were indicative of four lake salinity categories: freshwater, subsaline, hyposaline, and mesohaline. Most of the variation in the chironomid communities could be attributed to the loss of taxa in lakes with higher salinity. Observations also suggested that groundwater upwelling along the margins of lakes with extreme salinity could possibly allow small populations of chironomids to survive in littoral zones. Climate change and watershed disturbance are already altering water quality in western Mongolian lakes, and our results establish a baseline for chironomid communities along gradients of salinity and temperature by which future studies may be compared.