Pesticides can enter surface waters via different routes, among which runoff driven by precipitation or irrigation is the most important in terms of peak concentrations. The exposure can cause direct effects on all levels of biological organisation, while the toxicant mode of action largely determines which group of organisms (primary producers, microorganisms, invertebrates or fish) is affected. Due to the interconnectedness of freshwater communities, direct effects can entail several indirect effects that are categorised and discussed. The duration of effects depends on the recovery potential of the affected organisms, which is determined by several key factors. Long-term effects of pesticides have been shown to occur in the field. However, the extent of the effects is currently uncertain, mainly because of a lack of large-scale data on pesticide peak concentrations. In the final section, we elucidate the different approaches to predict effects of pesticides on freshwater ecosystems. Various techniques and approaches from the individual level to the ecosystem level are available. When used complementary they allow for a relatively accurate prediction of effects on a broad scale, though the predictive strength is rather limited when it comes to the local scale. Further advances in the risk assessment of pesticides require the incorporation and extension of ecological knowledge.