1. The application of fungicides is considered an indispensable measure to secure crop production. These substances, however, may unintentionally enter surface waters via runoff, potentially affecting the microbial community. To assess such risks adequately, authorities recently called for suitable test designs involving relevant aquatic microorganisms. 2. We assessed the structural and functional responses of leaf-associated microbial communities, which play a key role in the breakdown of allochthonous leaf material in streams, towards the inorganic fungicides copper (Cu) and elemental sulphur (S). These substances are of particular interest as they are authorized for both conventional and organic farming in many countries of the world. We used the food-choice of the amphipod shredder Gammarus fossarum (indicative for microorganism-mediated leaf palatability) as well as microbial leaf decomposition as functional endpoints. Moreover, the leaf-associated microbial communities were characterized by means of bacterial density, fungal biomass and community composition facilitating mechanistic understanding of the observed functional effects. 3. While Gammarus preferred Cu-exposed leaves over unexposed ones, microbial leaf decomposition was reduced by both Cu and S (up to 30%). Furthermore, Cu-exposure decreased bacterial densities (up to 60%), stimulated the growth of leaf-associated fungi (up to 100%) and altered fungal community composition, while S did not affect any of the assessed structural endpoints. 4. Synthesis and applications. We observed both structural and functional changes in leaf-associated microbial communities at inorganic fungicide concentrations realistic for surface water bodies influenced by conventional and organic farming. Our data hence justify a careful re-evaluation of the environmental safety of the agricultural use of these compounds. Moreover, inclusion of an experimental design similar to the one used in the present study in lower-tier environmental risk assessments of antimicrobial compounds may aid to safeguard the integrity of aquatic microbial communities and the functions they provide.