Display omitted •Water quality data (n > 8.3 mio) from 31 European countries (2001–2015).•Detection frequencies of organic contaminants (e.g. pesticides) increase over time.•Ecological thresholds are exceeded frequently in surface waters throughout Europe.•Ecological risks increase over time with pesticides being an important risk driver.•Monitoring data and water quality need improvements across Europe. 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 risks significantly increased over time for fish (τ = 0.498, p = 0.01) and aquatic invertebrates (τ = 0.429, p = 0.03). This indicates an increased chemical pressure to Europe’s waterbodies and overall large-scale threshold exceedances. Pesticides were identified as the main risk drivers (>85% of RTL exceedances) with aquatic invertebrates being most acutely at risk in Europe. Agricultural land-use was clearly identified as the primary spatial driver of the observed aquatic risks throughout European surface waters. Issues in monitoring data heterogeneity were highlighted and also followed by subsequent improvement recommendations, strengthening future environmental quality assessments. Overall, aquatic ecosystem integrity remains acutely at risk across Europe, signaling the demand for continued improvements.