The cold temperate helocrenes are usually attributed to high biodiversity because of environmental heterogeneity. Their temporal stability of environmental conditions reduces seasonal changes in assemblage composition. However, the within-site patterns and processes have been only rarely studied in springs, thus our knowledge remains limited. In this study, we investigated a microcrustacean assemblage of a helocrenic calcareous spring at a high spatial resolution. We tested differences among visually distinct mesohabitats, and related the assemblage composition variation to environmental variables and seasonal changes by a repeated sampling in spring, summer and autumn. At this single site, we recorded 26 species of ostracods and harpacticoids, accounting for almost 50% of the whole known regional species pool. Species richness and composition varied significantly between the mesohabitats, the latter mainly due to differences in environmental variables (mainly water depth and temperature). The occurrence of cold-adapted species was restricted to the spring source, but species inhabiting other mesohabitats had clearly broader ecological niches. Despite significant temporal changes in water temperature, microcrustaceans showed almost negligible seasonal changes in species composition, suggesting that their microdistribution remains stable throughout the year. Our findings have important implications for sampling design of large-scale ecological studies and spring conservation.