Despite their ecological importance, mosses remain under-represented in studies and conservation policies, mainly due to the specific and highly qualified expertise required for their identification. Molecular-based monitoring may represent a new advance in our understanding of these particular taxa. We evaluated the effectiveness of eDNA metabarcoding in detecting riverine and riparian bryophytes from river water samples. Our study is the first comprehensive evaluation of hybridization capture (HC) versus PCR-based eDNA metabarcoding, using vascular plant and bryophyte-specific primers, for bryophyte monitoring and in comparison with field surveys. The bryophyte-specific PCR method (bryoPCR) identified 101 species, 16 if which were shared with the HC method, and 37 with field surveys. The capture-based method retrieved 27 species, 9 of which were unique to the method and 11 common with the field surveys. Both eDNA methods identified bryophyte species that were not recorded in the field surveys but are known from the catchment. Although bryoPCR provided more species than HC, both methods exhibit comparable taxonomic resolution at the specie level. Each method outlines a unique composition of the community when applied to the same sites. Factors such as primer specificity and amplification bias contribute to the variation observed in the species composition detected. Our results highlight the importance of exploring the methodological variability of eDNA approaches before interpreting ecological patterns. In addition, we show the importance of identifying and developing tailor-made primers for studies on bryophytes to improve detection and the reliability of these studies. The capture-based method requires further optimization before considering it for eDNA applications.