A field survey of 196 sites on rivers across the Dinaric Ecoregion of Croatia revealed 61 sites (31.12%) in which bryophytes were the dominant part of the macrophyte vegetation. The Dinaric Ecoregion encompasses two subecoregions – Mediterranean (109 sampling sites, 26 bryophyte dominated) and Continental (87 sampling sites, 35 bryophyte dominated). Using classification and ordination analyses, we obtained three community types segregated across the gradients of climatic, physiographic and water chemistry parameters. The Didymodon tophaceus–Apopellia endiviifolia and the Berula erecta-Cratoneuton filicinum communities were associated with more basic and alkaline clean water with low nutrient content, biochemical oxygen demand and high dissolved oxygen. They were confined to the karstic rivers of the Mediterranean Subecoregion. Didymodon tophaceus–Apopellia endiviifolia community is a tufa-forming community associated with seasonally dry watercourses of small catchment areas, as well as cascades along the karstic rivers, characterised by a higher share of hygrophytes and turfs, while Berula erecta-Cratoneuton filicinum community was associated with Mediterranean rivers with a larger catchment area and permanent flow. It was characterized by a high share of rheophyte and aquatic species. The Cinclidotus community was the most widespread and associated with the karstic rivers of the Continental Subecoregion with intermediate values of water quality parameters and climatic variables associated with precipitation and water availability. The Continental Subecoregion of the Dinaric Ecoregion, with 40.23% bryophyte dominated sampling sites and 45 bryophyte taxa represents the diversity centre of freshwater bryophyte communities in Croatia.