|Spring fens are isolated treeless wetlands of a high conservation value. Their environmental conditions are strongly related to their groundwater chemistry, which controls species distribution within various groups of organisms. Clitellates, a dominant group of non-insect aquatic fauna, however, have never been studied in these habitats. It is unclear from previous studies to what extent the distribution of aquatic non-insect taxa reflects water chemistry rather than the substrate structure.We studied 34 spring fens sampled in 17 isolated sites in the Western Carpathian Mountains to determine mainly the effects of water chemistry and substrate structure on variation in species richness and composition of clitellate assemblages as examples of the non-insect fauna. A total of 34 taxa were found, with 3–15 taxa collected per sample. Species richness was negatively correlated with water mineral concentration measured as water electric conductivity (r = -0.57) and positively with TOC (r = 0.60). Surprisingly, the lowest number of taxa was found in calcareous fens and richness increased towards Sphagnum- fens. There was a species turnover related to changes in mineral richness and substrate characters. The main change of species composition was promoted by changes in substrate structure. The second gradient of species composition was linked with the amount of nutrients, moisture, and dominance of sphagna, and was associated with an increase of eurytopic species in fens with high nutrient availability. It was difficult to separate the effects of water chemistry and substrate on clitellate species distributions owing to the fact that variation in tufa precipitation and vegetation was driven by water chemistry changes. This study presented the first quantitative data on fen clitellate assemblages, which appear to have an unusual pattern of species richness. In contrast to plants and molluscs, calcareous fens appeared to be a harsh environment for clitellate species. Only few specialized species, mainly Trichodrilus strandi, were able to establish viable populations. The significant effect of water chemistry on clitellate distribution patterns raises questions about the direct influence of water chemistry on non-insect aquatic taxa, which have previously been considered to be mostly determined by substrate characteristics.