The study presents the results of lichenological research conducted in 2012–2016, based on my fieldwork carried out in mountain streams in the Polish Western Carpathians, revision of herbarium materials, and published data on lichen species in freshwater habitats in the study area. Field work was performed on 98 research plots divided into three zones related to duration of immersion (294 sampling sites in total). As the result of the work, 94 freshwater lichen species were found (91 based on my field work and/or revision of herbarium material), including 56 aquatic species. For all species, detailed descriptions of morphological and anatomical characters, information on their habitat, occurrence in the study area, worldwide and country distribution, and brief taxonomic notes are given. A key for species identification is also provided. From the present lichenological study, Verrucaria acrotella is reported as new for the Polish Western Carpathians. In total, 30 new species were recorded in particular mountain ranges in the study area. New records of Sarcogyne privigna and Thelidium fontigenum, very rare species in Poland, are given. The streams of the Polish Western Carpathians are characterized by high species diversity in various mountain ranges. The richest lichen biota was observed in streams of the Tatra Mts, where 76 species were found, representing more than 80% of the total number of freshwater lichens known from the Western Carpathians. In the Beskidy Mountains, species diversity in the streams remains within the range of 38–46 species. Two mountain ranges are distinguished by the presence of more species: the Beskid Sądecki Mts (60) and Beskid Żywiecki Mts (57). Thirtysix taxa were noted in the Carpathian foothills. A frequency analysis of lichens shows that very rare species (38 taxa; 40%) and rare species (32; 35%) dominate in the study area. Frequent lichens are the poorest group in the Polish Western Carpathians, accounting for only 4 species (slightly over 4%). Of all the lichens noted in the study area, 34 (~36%) are on the red list of the lichens in Poland. In the case of Carpathian streams, the substrate and the duration of inundation seem to be the most important factors for the occurrence of freshwater lichens. The duration of immersion also affects the species distribution. The submerged zone was the least diverse, in the terms of both number of species and represented families. The only species found there exclusively in the submerged zone were Ionaspis lacustris, Sporodictyon cruentum, Staurothele fissa, Thelidium submethorium, Verrucaria devensis and V. pachyderma. The splash zone provides a habitat transitional between the submerged and riparian zones. Lichens in this zone are constantly exposed to frequent changes between periods of inundation and desiccation. In the splash zone, both species found in the submerged zone as well as those occurring in the riparian zone were found. Species typical for the splash zone included Bacidina inundata, Gyalidea rivularis, Thelidium fontigenum, T. pluvium, Verrucaria humida and V. sublobulata. The most diverse group of lichens was associated with the riparian zone. Many lichens found in this zone are terrestrial lichens commonly found in non-freshwater habitats. They are considered to be rare in aquatic and semi-aquatic habitats but frequent in terrestrial habitats.