The new data here presented allow the reinforcement of the overall knowledge about distribution patterns and niche definition of some aquatic and semi-aquatic bryophytes of chorological and conservation interest (mosses: Cyclodictyon laetevirens, Dendrocryphaea lamyana, Fissidens fontanus, Hookeria lucens, Orthotrichum rivulare, Racomitrium hespericum, Racomitrium lamprocarpum and Schistidium rivulare; hepatics Barbilophozia barbata, Pallavicinia lyellii, Porella pinnata and Radula holtii). These species, considered rather vulnerable to hydrologic changes and with a threat status, were re-evaluated recently in the new Portuguese Atlas and Red Data Book and had extensive updates in their total distribution due to more recent efforts in herbarium revision and field studies in Portugal. As a result, we bring their distribution and auto-ecology up to date based on older records and new collections, showing the importance of systematic and extensive studies to narrow the definition of niches of taxa living in the ecotone amongst the aquatic and terrestrial environments. In the future, the improved field recognition of these taxa primary and secondary microhabitats and the protection of the mesohabitats with which they are associated will be the crucial steps for achieving their conservation at national level.