From eDNA signals to policy-relevant indices: a large-scale case study integrating molecular biodiversity monitoring into ecological quality assessment of lowland rivers

Accurate biodiversity indicators are essential to track ecosystem health, detect early signs of degradation, and guide effective conservation policy. Within the EU Water Framework Directive (WFD), ecological indices such as the fish-based Index of Biotic Integrity (IBI) serve as key tools to translate monitoring data into management-relevant scores. However, conventional electrofishing, though well established, faces limitations including restricted spatial coverage, seasonal and detection biases, and increasing ethical concerns. Environmental DNA (eDNA) metabarcoding has emerged as a promising alternative, yet its integration into standardized policy frameworks requires robust validation.

We present the results of a large-scale case study across 59 Flemish lowland river sites, where eDNA metabarcoding was benchmarked against electrofishing. By comparing biodiversity detection, seasonal consistency, and resulting ecological quality ratios (EQRs), we demonstrate that eDNA consistently detects higher species richness, including rare and cryptic taxa overlooked by traditional surveys. At the same time, electrofishing provides unique insights into population structure and recruitment, underscoring the complementarity of both approaches. Importantly, eDNA-derived ecological indices proved highly comparable to abundance-based WFD assessments, and they responded sensitively to habitat pressures across the landscape.

Building on these findings, we outline two pathways for embedding molecular methods into biodiversity policy metrics: (1) recalibration of existing IBI metrics per detection method to ensure methodological fairness, and (2) development of dedicated eDNA-based indices underpinned by standardized quality controls and transparent reporting. Such approaches enable eDNA to significantly upscale monitoring networks in both spatial coverage and temporal resolution, while targeted electrofishing continues to safeguard demographic information critical for management.

This hybrid monitoring framework demonstrates how molecular biodiversity measurements can be translated into robust ecological indicators. Beyond the WFD, the approach offers a blueprint for integrating eDNA into global biodiversity observation systems and emerging legislative frameworks such as the EU Nature Restoration Law. By combining sensitivity, scalability, and policy relevance, eDNA-based indicators can help accelerate biodiversity assessment and support evidence-based decision-making in freshwater conservation.