Knowledge of factors affecting the diversity of benthic invertebrates is very important for biodiversity conservation, for monitoring, restoring and maintaining aquatic ecosystems. The purpose of this study was to investigate how the diversity and distribution of freshwater mollusks related to environmental factors. Twelve species of freshwater mollusks were identified during a survey of 15 thermokarst lakes in the Gydan Peninsula, Russia. Canonical correspondence analysis (CCA) was used to study the relationships between environmental variables and species abundance. The first CCA axis correlated with the content of macro-ions, mainly Mg²⁺, Na⁺, Cl⁻, substrate types, and plant remnants. Along the second CCA axis stations were ordered by depth and the presence of mosses. We found that the type of substrate, depth, abundance of mosses and hydrochemical parameters play an important role in the distribution of the mollusks in thermokarst lakes. These results expand our understanding of mollusks ecology in thermokarst lakes, and identify environmental stressors important for the performance of abiotic control.