Abstract As a major ecosystem type, wetland provides invaluable ecological services. Environmental pollution, especially pesticides pollution should be paid more attention to keep wetlands healthy. Based on the risk quotient method, coupled with a probabilistic risk assessment model, this paper proposed a methodology suitable for ecological risk assessment of pesticide residues for wetland ecosystems. As an important industrializing and ecologically vulnerable area in China, the Taihu Lake wetland was chosen for the case study. The risks of eight pesticides in Taihu Lake wetland were assessed, as single substances and in mixtures. The assessment indicates that risks of the representative species are not significant. In general, the herbicide is found to be more toxic for algae, whereas insecticides pose more risks to zooplankton, insect and fish. For each pesticide in the wetland, the ecological risk it poses is acceptable. But the combined ecological risk posed by mixture can harm more than 10% of species of the wetland ecosystem, mainly dominated by dichlorvos, dimethoate and malathion contributions. These results imply that pesticide residues have been posing pressures on the ecosystem of the Taihu Lake wetland. It is recommended that proper countermeasures should be implemented to reduce the risks.