A floristic and ecological survey was carried out in 187 watercourses of the Portuguese Northwest mainland and Sicó mountain regions located in the transition zone between Atlantic and Mediterranean territories. This work mainly focused on the update of the bryophyte taxa along fluvial and geologic gradients, mostly of headwater areas. Seven ecological aspects (type of river segment, micro-habitat, immersion level and water velocity, depth range, shade, lithology and altitude) were classified and used to describe taxa autoecology. This survey is the first to present a comprehensive floristic catalogue and information on Portuguese aquatic and semi-aquatic taxa distribution. A list of 140 bryophytes was established for the studied areas, with predominance of mosses (102 taxa of mosses, 37 taxa of liverworts and 1 taxon of hornworts). Racomitrium aciculare, Platyhypnidium lusitanicum, Hyocomium armoricum, Scapania undulata and Fissidens polyphyllus were the most common taxa and Brachytheciaceae, Grimmiaceae and Fissidentaceae were the most frequent families in the studied micro-habitats. We updated the regional distribution of 30% of the taxa to new provinces of the Portugal. Four mosses and three liverworts are European endemisms, and Racomitrium (R. hespericum and R. lusitanicum) are, Iberian endemics. Distribution maps for selected species (Atlantic, dominant or rare species) are also presented.