There is a paucity of large-scale field investigations on the effects of organic toxicants on stream macroinvertebrate community structure and ecosystem functions. We investigated a total of 29 streams in two study areas of France and Finland for pesticide exposure, invertebrates and leaf-litter breakdown. To link pesticide exposure and community composition we applied the trait-based Species At Risk (SPEAR) indicator system. In the French region, pesticide stress was associated with a decrease in the relative abundance and number of sensitive species in the communities. The presence of undisturbed upstream reaches partly compensated the effects of pesticide contamination. Functional effects of pesticides were identified by a 2.5-fold reduction of the leaf-litter breakdown rate that was closely correlated with the structural changes in the contaminated streams. No effects of pesticides were observed in Finnish streams since contamination with pesticides was very low. In a follow-up analysis, the SPEAR approach successfully discriminated between reference and contaminated sites across different biogeographical regions, also including results of a previous field study in North Germany. Furthermore, change of the community structure was detectable at a concentration range as low as 1/100 to 1/1000 the acute 48 h-LC50 of Daphnia magna. Our findings demonstrate that pesticides may influence the structure and function of lotic ecosystems and that the SPEAR approach can be used as a powerful tool in biomonitoring over large spatial scales.