The research was carried out in calcareous fen habitats which share coverage with Natura 2000 sites designated under the EU Habitats and the Birds Directive. A total of 27 taxa of molluscs were recorded: 23 gastropod and 4 bivalve species. Anisus vorticulus, one of the species of Community interest whose conservation requires designation of special conservation areas within the Habitats Directive Natura 2000, was subrecedent and accedent in mollusc communities. Calcareous fen habitats offer the aquatic organisms harsh environmental conditions including a relatively high temperature of the water up to 33.29 °C (undrained fens), oxygen deficits in the water, high pH of up to 11.08 (fen pools) and conductivity above 3000 μS cm−1 (fen ditches). Therefore molluscs have to face extreme environmental conditions. Temperature of the water, pH, dissolved oxygen and conductivity were the parameters most associated with the distribution of mollusc species in the calcareous fen habitats. The abundance of submerged and floating macrophytes, the degree of habitat persistence and the fish predation pressure on molluscs also exerted a significant effect on their distribution. The calcareous fen habitats that are listed in Annex I of the European Union Habitats Directive create a unique valuable ecosystem that contributes to the natural diversity of aquatic organisms.