On Friday 13th September 2024, WP3 of the eDNAqua-plan project hosted an in-person workshop on the final day of the General Assembly. This brought together participants to discuss standards for genetic reference libraries and environmental DNA (eDNA) data repositories. The workshop was structured into three main sessions. Firstly, invited presenter Till-Hendrik Macher gave an online seminar on the curation of reference databases. Secondly, two sessions of group discussions were held to cover five topics related to reference databases and eDNA repositories. These covered the storage of vouchers, DNA-material and DNA-barcodes, data and associated metadata (1), the taxonomic curation procedures (2), the machine-readable workflows and data standards for interconnectable libraries (3), the pre-processed metadata for eDNA sample collection and sequencing (4) and the processed metadata for eDNA bioinformatic analysis and data submission (5). In a final session, a summary of the different discussions was made to the entire group, which allowed all participants to be updated on the conversations they missed and contribute further to the topics discussed. Overall, the day was marked by engaging discussions across the different sessions. The combination of grouped and general discussions allowed participants to give their insights on the different topics, as well as allowed the different topic leads to get insights from a wide panel of participants. The various discussion points and outcomes are captured in the proceedings. These will serve the two tasks working on data standards for reference databases (T3.1) and eDNA repositories (T3.2) to elaborate their work plan and formulate their recommendations.