Aquatic environmental DNA (eDNA) studies have considerably taken off during the last 10 years, promptly establishing eDNA as a new approach to monitoring the ecological status of European surface waters. On the one hand due to the numerous biological methods based on aquatic species, on the other hand due to the development of group-specific primers that allowed discrimination between species or at least genera. Understandably, rapid achievements were made for animal groups that include a small number of species (fish, amphibians) whereas it is still in development for plants, due to the complexity of obtaining a universal barcode applicable to eDNA for the latter. Nonetheless, research in plant eDNA barcoding and metabarcoding is making significant progress, mainly expanding in the detection of plant species in freshwater ecosystems. With a multi-barcode eDNA metabarcoding approach in mind, we are preparing a plant DNA barcode reference library for our study area, the Northern Vosges Regional Natural Park. Drawing from this experience and supported by current publications, we focus on the strong connection between metabarcoding of plant eDNA and floristic inventories, local barcode libraries, and herbaria. Prior knowledge of species distribution and abundant genetic data are the key to increasing species detection through eDNA (Cordier et al. 2020). We ought to standardise this practice before eDNA metabarcoding of plants can cover large river basins and span through time. Following the consensus on a combination of barcodes for the plant kingdom, the most recurrent ones in freshwater eDNA studies include the plastid DNA trnL, matK, rbcL regions and the nrDNA internal transcribed spacers (ITS) although it is likely that new barcodes emerge from further research. To date, the selection of primers seems to be of utmost importance since they offer different properties based on the research question. Seminal efforts have focused on the development of species-specific assays based on tailor-made primers. These have demonstrated the reliability of eDNA to be used for monitoring the distribution of aquatic plant species. Today, three of the most common aquatic invaders, Elodea canadensis, Elodea nutalli and Hydrilla verticillata have now their own assays aiming to identify the earliest invasions (Gantz et al. 2018). On the contrary, “universal” primers, such as those from White et al. (1990) within the ITS, prove to be useful in metabarcoding studies where many plant species from differing families are involved (Coghlan et al. 2020). Despite the fast-moving research in aquatic plant eDNA, DNA barcode reference libraries still lack many species, hindering the progress of applying eDNA surveys to large river basins through metabarcoding. Such studies still rely heavily on building local genetic libraries which is extremely time consuming and require important taxonomic knowledge of species, encumbered by the polyphyly of aquatic plant groups.

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Providing reliable, cost‐effective data on species distribution is critical to ensuring biodiversity conservation. However, many species may go unrecorded by conventional surveys, especially in aquatic environments. Environmental DNA (eDNA) barcoding and metabarcoding are alternative approaches that could complete biodiversity estimates based on species observations. While eDNA surveys are being standardized for some animal groups (e.g., fish and amphibians), research on eDNA approaches for freshwater plant communities is just starting to bear fruit. Here, we synthesized the 22 studies that used eDNA barcoding and metabarcoding to survey plant biodiversity in freshwater systems. We present evidence that contemporary aquatic plants (macrophytes) and terrestrial plants can be detected in water and surficial sediment eDNA from lakes and rivers. The phenology (e.g., senescence) of the target taxa strongly influences species detection. The main application of eDNA barcoding targets the monitoring of invasive macrophytes, and barcoding assays are available for 14 taxa. The metabarcoding approach shows a range of applications: the detection of rare macrophytes, catchment‐scale floristic inventories, and sediment fingerprinting. Barcodes on the plastid genome (cpDNA) are preferred for both approaches: matK and trnH‐psbA for barcoding, trnL, and rbcL for metabarcoding. The intergenic transcribed spacer 1 (ITS1) from the nuclear ribosomal DNA (nrDNA) was used for designing eDNA barcoding assays on five invasive macrophytes. In contrast, only three metabarcoding studies used the ITS1 or IST2 with newly designed primers. However, metabarcoding applications should routinely use a multi‐locus approach, combining cpDNA and nrDNA barcodes. Barcode combinations and existing primers need further testing on eDNA samples. We recommend using local barcode reference databases (BRDs), ideally self‐made, to circumvent taxonomic gaps and heterogeneous sequences in public BRDs. Finally, new technologies and developments like droplet digital PCR and hybridisation capture offer new perspectives for eDNA‐based biodiversity monitoring approaches.