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Aquatic ecosystems are at risk of being impaired by various organic chemicals, however comprehensive large-scale evaluations of waterbodies’ status and trends are rare. Here, surface water monitoring data, gathered as part of the EU Water Framework Directive and comprising the occurrence of 352 organic contaminants (>8.3 mil. measurements; 2001–2015; 8213 sites) in 31 European countries, was used to evaluate past and current environmental risks for three aquatic species groups: fish, invertebrates, plants. Monitoring quality indices were defined per country and found to improve over time. Relationships became apparent between countries’ monitoring quality index and their success in detecting contaminants. Across the EU, contaminants were more frequently found in recent years. Overall, 35.7% (n = 17,484) of sites exceeded at least one acute regulatory threshold level (RTL) each year, and average …