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Even though empirical data supporting sound ecoregion-specific ecotoxicological evaluations are still scarce, the differences of environmental (including climatic) conditions in specific ecoregions are already currently being regulated for environmental risk assessment of pesticides in Europe. To shed new light on the ecotoxicological effects of pesticides on aquatic communities across ecoregions, the model pollutant pyrimethanil (fungicide) was tested in an outdoor mesocosm study with macrophyte-dominated communities in the European "South" (Portugal) and "Centre" (Germany) regulatory zones. Phytoplankton indicators monitored over 12 months indicated a low risk of the fungicide (0.73 or 0.77 mg pyrimethanil L-1, single application) to phytoplankton functioning; as expected since exposure simulated worst-case scenarios. However, the growth of key structural macroalgae and macrophytes was affected by the fungicide and negative effects occurred, especially in the Central zone experiment. Such effects were not detected earlier than approximately nine months post single pyrimethanil application. The presence or absence of such extremely long-lasting/delayed pyrimethanil effects depended on species, competitive situation, and ecoregion-specific physico-chemical environment. The present findings suggest that a better understanding of both direct and indirect effects of fungicide pollution on aquatic flora in two European ecoregions helps to consolidate the environmental risk assessment of pesticides in specific regulatory zones. (c) 2019 Elsevier B.V. All rights reserved.