Aims and Background Groundwater-dependent minerotrophic fens are globally threatened biodiversity hotspots. The supply of groundwater keeps their soil thermally stable and mitigates climatic extremes by thermal buffering. This stability has been shown to influence species composition variation at the between-site scale but has not been studied at the within-site scale. Methods A total of 19 calcareous fens in the Western Carpathians were sampled for bryophytes, vascular plants, and terrestrial snails with three plots at each site along a watertable gradient, i.e. from the most waterlogged (plot A) through intermediately waterlogged (plot B) to the most terrestrial (plot C). Temperature dataloggers were buried in each plot, and climate variables were derived from the climate database. Results Water table depth and soil temperature were the most important factors influencing species composition. Significant differences were found between spring source area and fen margin plots for all taxa groups studied. Soil temperature played a significant role at the site level only for bryophytes and vascular plants. However, a large overlap between water table depth and soil temperature for bryophytes also suggests a synergistic effect of these two factors. Conclusion Soil temperature plays an important role in promoting compositional variation of vegetation on the within-site scale (i.e., a pure effect of soil temperature) in groundwater-dependent mires, as we show here for the first time. This is essential in the light of ongoing climate change. Conservation measures should primarily focus on bryophytes as they are the most temperature-sensitive organisms and important ecosystem engineers.