An extensive macrophyte field survey of running and standing waters was conducted from 2016 to 2021 at 786 sampling sites across Croatia as a part of the implementation of the Water Framework Directive. This survey is the first to present a comprehensive floristic catalogue of the freshwater bryoflora, along with an analysis of the distribution and diversity patterns on a national level. In all, 83 bryophyte species (68 mosses and 15 liverworts) were recorded in the 228 sites, with average species richness of 4.17 species per site. The most frequent species were Fontinalis antipyretica, Rhynchostegium riparioides, Leptodictyum riparium and Cratoneuron filicinum. The majority of the species encountered were rarely found, with over 70% of species recorded on less than 10 sampling sites and the majority of the species not being truly aquatic, rather being classified as facultative aquatics. The Dinaric Ecoregion, characterised by clean, cold, fast-flowing karstic rivers, especially in the Continental Subecoregion, supported higher freshwater bryophyte diversity than the lowland Pannonian Ecoregion, with mostly slow, eutrophic lowland watercourses with unstable sandy and gravelly alluvial sediments. Chorological comparison of Croatian eco- and subecoregions revealed the expected dominance of circumpolar and European elements, i.e. temperate chorotypes, as well as some biogeographical differences. The most frequent life forms were aquatic trailings and turfs. Amongst the recorded species, perennials and colonists were the most represented life strategies. The analysis of both the life-form and life-strategy spectra showed some differences amongst the Croatian regions, supporting the fact that the Dinaric Ecoregion provides more truly aquatic habitats and microhabitats suitable for the freshwater bryophytes, while in the Pannonian Ecoregion freshwater bryophytes dominantly inhabit the periodically submerged riparian zones, for example shaded lowland forest streams and rivulets or gently sloping margins of rivers and lakes.