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Aquatic biota in Central Asia witnesses and faces a changing environment. Because ostracodes contribute to both extant and fossil lacustrine diversity, they can be used to track evolution in water quality. Living ostracode communities in a variety of aquatic habitats of western Mongolia were analyzed in relation to environmental and hydrochemical variables of those habitats, based on presence/absence data from net samples. The sampled water bodies represent broad gradients in ionic concentration and composition. Ostracode community composition of springs differed from all other sampled habitats, which was also reflected in CCA analyses. Our data indicated that the ostracode fauna of western Mongolia shows a high response to calcium content, alkalinity, salinity, temperature, nutrients, and altitude. Species composition and diversity seem to be determined by solute evolution dominated by Ca-depletion. In general, this seems to be an important regulator of lacustrine ostracode species composition in several semi-arid regions. Binary logistic regression was used to predict the occurrence of the most common species with a minimal set of environmental variables. The resulting models showed on average low performance, and mainly demonstrated the potential of such modeling to predict the distribution of typical bio-indicator species.