The eDNAqua-Plan WP3 workshop, held on the 5th of February 2025, brought together eDNA experts and stakeholders to conceptualize and improve the eDNA data ecosystem. Participants examined the current landscape of reference libraries, eDNA data publishing, and biodiversity databases, identifying key challenges such as metadata inconsistencies, limited taxonomic curation, and fragmented data flows. For reference libraries, the need for common taxonomic curation principles and a core set of essential metadata were emphasized. For eDNA data publishing, a set of common controlled vocabulary(particularly bioinformatics), better data submission and handling guidelines are needed. Overall, data and metadata flows need to be improved, with tailored approaches for research and national monitoring need to be considered. Looking ahead, participants envisioned an ideal eDNA ecosystem comprising a network of taxonomically curated reference libraries, accessible via a centralized data portal. Recommendations included promoting standardised metadata practices, developing accreditation frameworks for reference databases, training stakeholders in FAIR principles and fostering stronger links between research and national monitoring initiatives. The workshop also emphasised reducing ecosystem fragmentation by consolidating standards and implementing quality-control schemas for data fitness. The workshop outcomes will inform WP3’s Deliverables, Milestone M3.3 and support WP5’s blueprint and roadmap for future system implementation. In this way it will contribute to shaping a more efficient and FAIR eDNA data ecosystem and ultimately support the advancement of biodiversity monitoring across Europe.