Data from more than 4000 freshwater monitoring sites showed that in more than 14 per cent, organic pollutants were likely to be killing off fish, invertebrates and algae.
Chronic long-term effects of pollution were expected to be having an impact in 42 per cent of the sites.
Scientists measured concentrations of the chemicals at 4001 sites distributed over 91 European river basins.
The scientists, led by Egina Malaj, from the Helmholtz Centre for Environmental Research in Leipzig, Germany, wrote in the journal Proceedings of the National Academy of Sciences: "Our results clearly indicate that chemical pollution is a large-scale environmental problem and requires far-reaching, holistic mitigation measures to preserve and restore ecosystem health."
Regionally, river basins in the north of Europe were more at risk from pollution than those in the south.