Despite numerous ecological studies with mosquitoes, it remains unclear what environmental factors are the most important determinants of structure, species richness, and abundance of mosquito assemblages. In the current study, we investigated relations between these characteristics of mosquito larvae assemblages and environmental factors in a large set of different habitats. Particular objectives were (1) to rank the factors regarding their explanatory power, and (2) to quantify the contribution of major sets of factors such as habitat spatial/hydrological (H), water physico-chemical (W), and aquatic vegetation characteristics (V). Variance partitioning and forward selection based on ordinations and multiple regressions were applied to the data set on 79 water-bodies in southwestern Siberia covering a wide gradient of environmental characteristics and diverse mosquito assemblages. The results showed that richness and abundance inter-correlated poorly (r² = 0.21), and assemblage structure, richness, and abundance depended on different sets of predictors. Explanatory importance of the three sets of environmental factors differed among the three assemblage variables: H, W, and V had equal importance for assemblage structure, while richness and abundance depended on H and V more than on W. The study showed that contradiction between the aims of conservation (support biodiversity) and mosquito control (reduce mosquito abundance) can be avoided, as relevant environmental factors can be used to define habitats with high richness and low abundance (i.e., high conservation value and low nuisance and disease transmission risk) for conservation activities, and conversely for control measures.