Environmental DNA (eDNA) metabarcoding is transforming biodiversity monitoring, particularly in aquatic environments. The current most common approach uses PCR to specifically amplify the DNA of target taxa. As with any approach, PCR-based metabarcoding has inherent biases that significantly influence the set of species that can be detected. Hybridization capture (HC), or target enrichment, is a promising alternative to PCR-based eDNA metabarcoding as it overcomes some of the biases associated with PCR. We evaluated the effectiveness of HC metabarcoding in detecting plant species from water samples across diverse river types, from oligotrophic headwaters to large floodplain rivers. Our study is the first comprehensive evaluation of HC eDNA metabarcoding using four common plant markers (trnL, rbcL, ITS2, ITS1), directly comparing it to PCR-based metabarcoding and field surveys for aquatic vegetation diversity monitoring. The same river water samples, bioinformatic pipeline and reference database were used for the two eDNA approaches, such that differences between the methods arise from their intrinsic properties. Our findings show that HC recovers comparable species richness to PCR-based metabarcoding, detecting taxa across the four main plant phyla. For instance, HC recovered a significant number of mosses, which are often difficult to identify and frequently overlooked in vegetation surveys but serve as important bioindicators. The three methods recover rare taxa but HC finds additional rare species, also missed in the field surveys. While both eDNA methods offer advantages over traditional field surveys, they also retrieved unique sets of species, highlighting intrinsic methodological biases. The use of one or the other will depend on the objectives of the study. By addressing key technological gaps in PCR-based methods, such as the detection of cryptic diversity and the limitations of primer universality, our study opens up new possibilities for eDNA-based biodiversity assessments. The presentation will discuss the advantages and limitations of hybridization capture, its implications for biodiversity monitoring, and propose strategies for integrating this technique into standard eDNA practices to overcome current challenges.