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Microbial decomposers play a crucial role in detritus-based freshwater food webs, yet their disruption by antimicrobial contaminants and the subsequent bottom-up effects on aquatic food webs remain poorly understood. This study investigates how the fungicide Azoxystrobin and the antibiotic Ciprofloxacin affect microbial leaf conditioning, indirectly impact macroinvertebrate community structure, and thus cause shifts of functional feeding groups in stream mesocosms. To this end, black alder leaves were conditioned in the presence of increasing concentrations of either Azoxystrobin or Ciprofloxacin. Subsequently, the conditioned leaves were transferred to stream mesocosms, colonized by macroinvertebrate communities from a least-impacted stream, where such leaves served as the primary food source. Azoxystrobin significantly reduced fungal biomass on leaves by up to 80%, likely leading to lower detritus quality, impaired conditioning, and cascading shifts in macroinvertebrate communities (p = 0.04). Gammarus fossarum as a dominant species in the studied mesocosm, increased in abundance contributing 18% to community dissimilarity with increasing Azoxystrobin-treated leaves most likely through dietary flexibility and compensatory feeding of leaves or other sources. Chironomidae (Orthocladiinae, Chironomini, Tanytarsini), in contrast, declined (24% dissimilarity contribution), likely due to their reliance on well-conditioned detritus. Shredders (29%), predators (18%), and scrapers (14%) contributed most to macroinvertebrate community differentiation, indicating trophic propagation beyond primary consumers, that is, shredders. In contrast to the fungicide, the antibiotic Ciprofloxacin did not induce significant changes, suggesting fungal decomposers are the primary driver of detritivore-mediated energy flow. These findings emphasize the critical role of microbial-mediated leaf decomposition in structuring freshwater food webs and highlight potential ecological risks associated with fungicide contamination at microbial level, but with impacts well exceeding the microbial communities.