Large amounts of fungicides are applied globally and partly enter freshwater ecosystems. A few laboratory studies examined their effects on decomposer communities and the ecosystem process of litter decomposition (LD), whereas the field situation remains largely unknown. We conducted a field study with 17 stream sites in a German vineyard area where fungicides represent the dominant pest control agent. Passive samplers were used to monitor 15 fungicides and 4 insecticides in streams and their toxicity was described using the toxic unit approach, whereas sediment samples were taken to characterise total copper concentrations. Microbial and leaf-shredding invertebrate community composition and related LD rates were assessed at each site. The structure of microbial and shredder communities as well as fungal biomass changed along the fungicide toxicity gradient. The changes in microbial endpoints were associated with a reduction of microbial LD rate of up to 40% in polluted streams. By contrast, neither the invertebrate LD rate nor in-situ measured gammarid feeding rates correlated with fungicide toxicity, but both were negatively associated with sediment copper concentrations. A subsequent laboratory experiment employing field fungicide concentrations suggested that the microbial community changes are causal. Overall, our results suggest that fungicides can affect LD under field conditions.