eDNAqua-Plan, started in September 2023, is a 36-month HorizonEurope-funded project. The project spearheads the collection of data on aquatic monitoring initiatives, evaluates standardisation efforts, and explores the potential for a FAIR-based digital ecosystem for eDNA repositories and a dynamic species reference library. This interdisciplinary initiative aims to assess existing projects, standardization efforts, and infrastructures for aquatic monitoring. By collaborating with EU research projects and infrastructures such as EMODnet, BIOSCAN-Europe, LifeWatch, and international systems like ELIXIR/EBI and OBIS, the consortium maximizes synergies and interoperability, contributing to a harmonized aquatic monitoring roadmap using eDNA tools in Europe and beyond.