In the last decades, land-use changes have made Mediterranean forests highly susceptible to wildfires, which can cause several impacts not only on burnt areas, but also on adjacent aquatic ecosystems. Post-fire runoff from burnt areas may transport toxic substances to streams by surface runoff, including polycyclic aromatic hydrocarbons (PAHs) and metals, which can be noxious to aquatic organisms. Impacts on aquatic ecosystems can be related to fire severity, forest type and the exposure period; however, these factors have not been investigated in tandem. Here, we used the stream detrital system to determine the impacts of post-fire runoffs and stream water from a burnt catchment on trophic interactions between stream microbial communities and invertebrate shredders involved in leaf litter decomposition. Three distinct types of samples were collected from a burnt catchment: post-fire runoffs from high severity wildfires in Pinus and Eucalyptus forests, and stream water. Microbial decomposer communities (fungi and bacteria) and the invertebrate shredder Allogamus ligonifer were exposed for 10 and 20 days to increasing concentrations (0, 50, 75 and 100%) of runoff extracts. Our results showed that post-fire runoffs from high severity wildfires reduced microbially-driven leaf litter decomposition (up to 79%), invertebrate feeding (up to 75%), fungal biomass (up to 39%) and altered community composition; effects were more severe at the longer exposure time. The impacts varied with the runoff source and were related to the chemical composition in metals and total PAHs. This study emphasizes the importance of assessing the indirect effects of wildfires taking into account the effects of the runoff source, load and exposure time on freshwater biota and their ecological functions. Therefore, best forest management practices should be applied to minimize post-fire runoffs reaching aquatic ecosystems and to reduce the effects of these extreme events on freshwater biodiversity and ecosystem functioning.