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Assessing climate change impacts on pesticide leaching requires careful consideration of different sources of uncertainty. We investigated the uncertainty related to climate scenario input and its importance relative to parameter uncertainty of the pesticide leaching model. The pesticide fate model MACRO was calibrated against a comprehensive one-year field data set for a well-structured clay soil in southwestern Sweden. We obtained an ensemble of 56 acceptable parameter sets that represented the parameter uncertainty. Nine different climate model projections of the regional climate model RCA3 were available as driven by different combinations of global climate models (GCM), greenhouse gas emission scenarios and initial states of the GCM. The future time series of weather data used to drive the MACRO model were generated by scaling a reference climate data set (1970-1999) for an important agricultural production area in south-western Sweden based on monthly change factors for 2070-2099. 30 yr simulations were performed for different combinations of pesticide properties and application seasons. Our analysis showed that both the magnitude and the direction of predicted change in pesticide leaching from present to future depended strongly on the particular climate scenario. The effect of parameter uncertainty was of major importance for simulating absolute pesticide losses, whereas the climate uncertainty was relatively more important for predictions of changes of pesticide losses from present to future. The climate uncertainty should be accounted for by applying an ensemble of different climate scenarios. The aggregated ensemble prediction based on both acceptable parameterizations and different climate scenarios has the potential to provide robust probabilistic estimates of future pesticide losses.