Owing to a long history of anthropogenic pressures, freshwater ecosystems are among the most vulnerable to biodiversity loss¹. Mitigation measures, including wastewater treatment and hydromorphological restoration, have aimed to improve environmental quality and foster the recovery of freshwater biodiversity². Here, using 1,816 time series of freshwater invertebrate communities collected across 22 European countries between 1968 and 2020, we quantified temporal trends in taxonomic and functional diversity and their responses to environmental pressures and gradients. We observed overall increases in taxon richness (0.73% per year), functional richness (2.4% per year) and abundance (1.17% per year). However, these increases primarily occurred before the 2010s, and have since plateaued. Freshwater communities downstream of dams, urban areas and cropland were less likely to experience recovery. Communities at sites with faster rates of warming had fewer gains in taxon richness, functional richness and abundance. Although biodiversity gains in the 1990s and 2000s probably reflect the effectiveness of water-quality improvements and restoration projects, the decelerating trajectory in the 2010s suggests that the current measures offer diminishing returns. Given new and persistent pressures on freshwater ecosystems, including emerging pollutants, climate change and the spread of invasive species, we call for additional mitigation to revive the recovery of freshwater biodiversity.

Reliable assessment of the ecological status of standing waters is key for the effective implementation of the Water Framework Directive and for supporting water management and conservation. Biological quality elements, including benthic macroinvertebrates, provide an integrated measure of ecological condition by reflecting the cumulative impacts of environmental pressures over time. However, assessment methods developed for running waters are not readily applicable to standing waters, highlighting the need for category-specific approaches. We conducted a large-scale survey of representative stagnant water bodies (lakes and reservoirs) on the territory of Bulgaria. The goal was to develop a relevant type-specific methodology for the ecological status assessment of standing waters based on macrozoobenthos. We sampled 79 monitoring lake sites between May and November 2020 through an adapted version of the multi-habitat sampling methodology developed within the European AQEM/STAR projects in accordance with applicable standards. A composite sample was taken from the littoral zone of lakes and reservoirs, representative of the substrates available at each location. The sites represent 19 lake types. Eleven biological indices for lakes and seven for rivers were calculated in order to identify the most suitable metric. For each of the metrics, the pressure–response relationship was estimated. Being the first operational national index based on macroinvertebrates, the proposed Bulgarian multi-metric index for lakes is an adapted version of the Hungarian multi-metric macroinvertebrate index. It consists of three metrics, which have been separately tested in Bulgaria for monitoring purposes as early as 2011–2012 as well as in subsequent scientific research. Ecological quality class boundaries for each type of water body were determined. The compatibility of the BMMI with the existing national monitoring programme would facilitate its future integration into the biological water assessment system.