Streams contamination by pesticides and nutrients, resulting from human activities, is widespread. However, the interactive effect of these two stressors on heterotrophic microbial communities and their activity of organic matter decomposition is still poorly understood. In this context, a microcosm experiment was performed to evaluate the single and interactive effects of environmental concentrations of the herbicide S-metolachlor and the fungicide tebuconazole, on the decomposition ability of leaf-associated microbial communities, in either eutrophic or mesotrophic conditions. Eight treatments were tested in triplicate to assess, in laboratory channels, the resulting effects on natural microbial communities from a pristine forested stream (Couze d’Ardes, Centre France) developing on Alnus glutinosa leaf species. Every week for 40-days, water was renewed and samplings were performed to measure Alnus leaves’ decomposition rates (Kday), as well as the structure (biomass and diversity) and enzymatic activities of the leaf-associated microbial communities. Results showed a stronger influence of nutrients compared to that of pesticides. Indeed, while decomposition rates, microbial biomass, fungal diversity and ligninolytic activities (laccase, phenol oxidase) were higher in eutrophic channels compared to mesotrophic ones, only a three-fold increase of laccase activity by tebuconazole was observed in eutrophic condition. Surprisingly, such activity increase was not observed in eutrophic conditions when the fungicide and the herbicide were mixed. Overall, our study shows that the effect of realistic environmental concentrations of pesticides on leaf-associated microbial communities can be negligible compared to the effect of nutrients. However, the tested tebuconazole concentration was sufficient to trigger physiological response in fungal community.