The diversity of spring habitats can be determined not only by local environmental conditions, but also by large-scale biogeographical effects. The effects can differ across various groups of organisms. We compared alpha-, beta- and gamma-diversity patterns of bryophytes and vascular plants of (sub)alpine springs in three contrasting mountain ranges: Alps (Switzerland), Balkans (Bulgaria), Western Carpathians (Slovakia, Poland). We used univariate and multivariate statistics to test for the effects of pH, conductivity, altitude, slope, mean annual temperature and annual precipitation on diversity patterns of both taxonomic groups and compared diversity patterns among the regions for particular pH and conductivity classes. We identified acidophyte and basiphyte, calcifuge and calcicole species using species response modelling. All regions displayed significant relationship between conductivity and alpha-diversity of vascular plants. Bulgaria showed the highest alpha-diversity of vascular plants for the middle part of the conductivity gradient. For both taxonomic groups, the beta-diversity in the middle part of gradient was highest in Swiss Alps. The total species pool was lowest in Bulgaria. The percentage of basiphyte and calcicole species was highest in the Alps. In (sub)alpine springs, mineral richness was a better determinant of vascular plant alpha-diversity than pH, and the extent of the alpine area did not coincide with alpha-diversity. Observed inter-regional differences in diversity patterns could be explained by the different proportion of limestone bedrock and different biogeographic history. The differences in alpha-diversity between both taxonomic groups are presumably result of the different rates of adaptation processes.