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Springs are unique and vulnerable habitats, which have always been rather out of focus of the scientist interest. Nevertheless, they frequently host very diverse and species-rich assemblages with high proportion of species more or less adapted to their unique environment and can act as biodiversity hotspots in some areas. The Western Carpathian springs are helocrene springs and represent wide variety of different habitat types, from mineral rich sparsely-vegetated or bryophytes-rich covered helocrenes to acidic peaty sites. Such diversification allows the creation of highly diverse assemblages, in which Chironomidae usually dominate in both species richness and abundance. The aim of this study was to provide a comprehensive overview of chironomid assemblages inhabiting the unique environment of spring fens and factors driving the metacommunity structuring and populations of individual taxa. We examined chironomid assemblages of 62 small, treeless helocrenes sites, which are highly isolated from each other by the terrestrial environment constituting dispersal barriers such as the east-west oriented mountain ridges and valleys. The sampling was performed to cover mesohabitat heterogeneity of study sites. Two main mesohabitats were sampled, the plot with flowing water and coarser substratum near water source (the lotic mesohabitat), and water-logged soil with standing water (the lentic mesohabitat). Study sites hosted nearly 100 chironomid taxa, both mesohabitats were inhabited by chironomid assemblages similar in number of species and abundances and the local environment was proved to be the main driver of compositional changes in chironomid assemblages as expected. Moreover, the significant spatial structure of assemblages was found at the lentic mesohabitat, while biotic interactions described by the abundance of Gammarus fossarum and taxa richness and abundances of predators did not significantly contribute to compositional changes in assemblages at any mesohabitat. Nevertheless, taxa-specific responses revealed populations of many taxa significantly affected by biotic interactions, especially at the more stable lotic mesohabitat, which is in concordance with suggested greater importance of biotic interactions at stable environment. Our results emphasized the importance of multilevel approach in community ecology for proper distinction between different mechanisms of metacommunity structuring. Biotic interaction such as competition can result into the same community patterns as environmental filtering, thus the involvement of detailed analyses of species requirements and interactions is necessary.