We analyzed the composition of spring fauna in relation to the mesoscale variability in environmental conditions in 77 permanent springs in a geologically homogenous area. We hypothesized that the species would occur in definite patterns reflecting the differences in factors that operate at the spring-level scale. We focused on the differences resulting from spring morphology, substrate composition, shading, and water chemistry. Our goal was to identify the abiotic variables that control the character of interspecies associations. The spring assemblages comprised species of 9 higher taxonomic groups (Plecoptera, Trichoptera, Coleoptera, Diptera, Turbellaria, Crustacea, Mollusca, Oligochaeta, Hydracarina). We used binomial regression successfully to construct single-species environmental models for several of the most abundant taxa. The most important factors explaining the species' occurrence were hydromorphological and substrate characteristics. Results of nonmetric multidimensional scaling ordination on species composition indicated 3 groups of springs. However, the analysis did not provide evidence for strong interspecies associations. Group 1 separated springs with running water, high substrate heterogeneity, and high taxonomic richness. Groups 2 and 3 included mostly helocrene-like springs differing in slope and substrate composition. The assemblages of these 2 groups comprised the same dominant species. However, the springs from group 3 had lower species abundances. Our study demonstrates the importance of mesoscale differences in habitat conditions for structuring the spring-associated benthic assemblages.