During the research of aquatic and semi-aquatic mosses, which included 786 sites on watercourses and standing waters, 83 bryophyte species (68 mosses and 15 liverworts) were recorded. This amounted to 12% of the so-far-known bryophyte diversity in Croatia. The karstic rivers of the Dinaric Ecoregion supported greater diversity compared to those of the Pannonian Ecoregion, where bryophytes were mostly restricted to river margins, which was supported by differences in the life-form and life strategy spectra between the ecoregions. Most species preferred clear, neutral to basic karstic watercourses with low levels of nutrients and organic matter, i.e. pristine watercourses with a high proportion of natural land in the catchment area. Among them, species with very narrow ecological niches were singled out and recognised as good and reliable bioindicators. However, the most abundant and widespread species had very wide ecological niches, while only two, Riccia fluitans and Leptodyctium riparium, preferred hypereutrophic watercourses with a high proportion of intensive agriculture in the catchment area. In natural watercourses, mosses were the dominant component of the vegetation in only 14.42% of the investigated localities, with the Dinaric Ecoregion, i.e. its cold, fast karst watercourses with larger and more stable substrates, representing the distribution and diversity centre of these bryophyte dominated communities. Five communities were identified, with three most represented being characteristics for the karstic watercourses of the Dinaric Ecoregion, and two for the small streams of the Pannonian Ecoregion. They differed in species richness and composition, the share of bryophytes and their affinity for water as well as in lifeform spectra. Furthermore, these communities were segregated along gradients of water chemistry (alkalinity and water quality), bioclimatic parameters related to water availability and its yearly distribution, as well as the size of the catchment area.