Insights from a comprehensive European survey

DNA-based approaches, including environmental DNA (eDNA) metabarcoding, are increasingly being explored to complement conventional biological monitoring of aquatic ecosystems. This report reviews current practices, experiences, and future perspectives regarding the use of DNA-based approaches for ecological status assessment under the European Union Water Framework Directive (WFD). To support this review, a questionnaire was distributed among EU Member States, associated countries, and stakeholders participating in the Common Implementation Strategy (CIS) ECOSTAT working group. The survey collected quantitative and qualitative information on the application of DNA-based methods across Biological Quality Elements (BQEs), ongoing research and monitoring activities, methodological approaches, perceived strengths and limitations, and future implementation needs. Responses from 26 countries and 17 stakeholder organisations indicate that, although operational implementation remains limited, the use of DNA-based approaches in research and pilot monitoring is widespread and expanding. DNA-based methods are most frequently applied to fish and macroinvertebrates, followed by diatoms and phytoplankton, with rivers and lakes being the primary focus. eDNA metabarcoding is the most widely used molecular technique, complemented by bulk metabarcoding and specimen barcoding. Respondents recognised the considerable potential of DNA-based approaches to improve ecological status assessment under the WFD, while identifying key barriers to wider implementation, including incomplete reference databases, limited quantitative information on abundance and biomass, methodological and bioinformatic challenges, costs, and regulatory uncertainty. The questionnaire findings were further discussed and validated during the CIS ECOSTAT online workshop, The future is now – (e)DNA for monitoring and assessing the Water Framework Directive, held on 21 November 2025, with more than 100 experts from scientific, policy, and regulatory organisations. Both the survey and workshop highlighted broad consensus that DNA-based approaches should be progressively integrated into WFD monitoring as a complement to conventional methods. Participants identified harmonisation, standardisation, quality assurance, intercalibration, reference database development, capacity building, and coordinated European pilot projects as key priorities for supporting their regulatory uptake. The report provides a European overview of current implementation and presents recommendations to support the gradual integration of DNA-based approaches into future WFD assessment frameworks.

VÖLKER Jeanette;  LIEBMANN Liana;  ARLE Jens;  VAN DRIESSCHE Charlotte;  VARKITZI Ioanna;  BEERMANN Arne;  BROOKE Jan;  BRYS Rein;  FELFÖLDI Tamas;  HOP Jochem;  JEANNOT Benjamin;  KAHLERT Maria;  LEESE Florian;  MEISSNER Kristian;  MINGARELLI Sandra;  RIMET Frederic;  SANDOY Steinar;  WAGNER Franz; 

2026-08-05

Publications Office of the European Union

JRC147441

978-92-68-42320-2 (online),   

1831-9424 (online),   

EUR 40799,    OP KJ-01-26-327-EN-N (online),   

https://publications.jrc.ec.europa.eu/repository/handle/JRC147441,   

10.2760/3791585 (online),