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Environmental DNA (eDNA) is reshaping aquatic biodiversity monitoring by enabling scalable, cross-ecosystem species detection. Its broader societal and scientific value, however, is constrained by fragmented data governance, inconsistent metadata practices, and limited interoperability between standards. eDNA data is produced by a wide range of actors using partially overlapping, but misaligned metadata standards, which hinders data discoverability, integration, reuse, and interpretation across systems and jurisdictions.This deliverable addresses these barriers through Task 3.2 of eDNAqua-Plan, which focuses on improving interoperability by aligning community (meta)data standards across the full aquatic eDNA biomonitoring workflow, from field sampling and laboratory processing to sequencing and bioinformatic analysis. Where relevant, it also accounts for the diversity of eDNA data types, including metabarcoding datasets, mitogenomes, and metagenomes.Stakeholder-driven use-case evaluations were used to assess the perceived importance and feasibility of metadata terms in real-world submission contexts. These evaluations provide evidence-based insight into current practices and inform recommendations on which metadata elements are primed for standardisation to balance (meta)data quality and reporting burden.The main technical outcome is two alignment models using the Simple Standard for Sharing Ontological Mappings (SSSOM). One aligns the GBIF/OBIS DNA-derived extension with Genome Standards Consortium (GSC) MIxS Core; the other formalises and updates the alignment between the Barcode Core Data Model (used by Barcode of Life Data Systems, BOLD) and MIxS Core. Together, these models enable practical interoperability while revealing structural misalignments, unclear term provenance, and coordination gaps between standards bodies and biodiversity infrastructures.The report also highlights the critical role of metadata in ensuring traceability, provenance, and adequate reuse of eDNA data. Persistent links between sequence data, source material, and spatiotemporal context are essential for data quality, reproducibility, and compliance with Access and Benefit Sharing frameworks, including the Nagoya Protocol and the Biodiversity Beyond National Jurisdiction agreement.Finally, the deliverable identifies governance challenges that must be addressed to ensure long-term impact, including sustained ownership and maintenance of alignment models beyond project lifetimes, stronger coordination between standards organisations, and mechanisms to manage misalignment as standards evolve.Overall, this deliverable provides immediate, actionable outputs through alignment models and practical recommendations towards a sustainable, interoperable European eDNA digital ecosystem. Improving metadata interoperability is a necessary prerequisite for the reliable, large-scale use of eDNA data in monitoring biodiversity and informing evidence-based policy.