The study is the first to compare regional biodiversity in polluted versus less polluted water, said scientists at the Helmholtz Association of German Research Centres. It was published in the US journal the Proceedings of the National Academy of Sciences.
Freshwater invertebrates and aquatic insects were 42 percent less common in strongly contaminated areas in Europe compared to less polluted areas; in Australia, a difference of 27 percent was found across regions.
The analysis included measurements of insecticides and fungicides, which are used often in agriculture and are typically well-studied and heavily regulated.
However, the researchers said little examination had until now been done to gauge their effect on the streams and rivers they end up in after it rains and the chemicals are washed off farmland and into watercourses.
"The current practice of risk assessment is like driving blind on the motorway," said ecotoxicologist Matthias Liess, a study co-author.
Species that were particularly vulnerable to pesticides included dragonflies, stoneflies, mayflies and caddis flies.
The researchers warned that the threat pesticides pose to biodiversity had been underestimated, since experimental work preceding a pesticide's market approval were laboratory-based or conducted on artificial ecosystems.
"The effects in Europe were detected at concentrations that current legislation considers environmentally protective," said the study, calling for new approaches to better assess the ecological risks of pesticides.
A better practice would be to assess the ecological impact of chemicals by investigating real environments on a larger scale, the authors said.
The findings show that UN goals to slow down the decline in biodiversity by 2020 are "jeopardized," it said.