Abstract
Freshwater ecosystems harbour disproportionate biodiversity yet face the most severe and accelerating decline of any
major biome globally. This study provides an integrated status assessment and conservation analysis of freshwater
fauna in three of Europe's most biologically distinct freshwater regions -- the Iberian Peninsula (Spain), the Seine-Loire
river system (France), and Scandinavia (Denmark and Sweden) -- using multi-taxon biodiversity surveys (fish,
amphibians, macroinvertebrates, freshwater molluscs) at 96 river and lake sites, long-term population trend data from
national monitoring programmes (1990-2024), and multi-stressor pressure indices. A total of 24,847 individual records
across 341 taxa were recorded. Freshwater biodiversity index (FBI) scores reveal that 60.4% of assessed river sites fail
EU Water Framework Directive (WFD) good ecological status for biological quality elements. Long-term trend analysis
shows that 58.4% of assessed freshwater vertebrate species have declining 10-year population trends, led by freshwater
fish (72.4% declining) and amphibians (64.8% declining). Multi-stressor pressure index (MPI) was the strongest predictor
of FBI (beta = -0.68 +- 0.08, p < 0.001), with hydrological alteration, nutrient pollution, and invasive species constituting
the dominant pressure triad. Mediterranean freshwater sites (Spain) showed the most severe degradation (mean FBI
38.4 +- 6.8 vs. Scandinavian reference 72.4 +- 8.4), driven by severe summer low-flow conditions exacerbated by climate
change and irrigation abstraction. Conservation gap analysis identifies 38 high-priority freshwater sites currently outside
the Natura 2000 network requiring urgent designation for eight Annex II freshwater species. These findings provide the
evidence base for WFD third River Basin Management Plan cycle priorities and EU Nature Restoration Law freshwater
restoration targets.