Fungi are important decomposers of leaf litter in streams and may have knock-on effects on other microbes and carbon cycling. To elucidate such potential effects, we designed an experiment in outdoor experimental channels simulating sand-bottom streams in an early-successional state. We hypothesized that the presence of fungi would enhance overall microbial activity, accompanied by shifts in the microbial communities associated not only with leaf litter but also with sediments. Fifteen experimental channels received sterile sandy sediment, minimal amounts of leaf litter, and one of four inocula containing either (i) fungi and bacteria, or (ii) bacteria only, or (iii) no microorganisms, or (iv) killed microorganisms. Subsequently, we let water from an early-successional catchment circulate through the channels for 5 weeks. Whole-stream metabolism and microbial respiration associated with leaf litter were higher in the channels inoculated with fungi, reflecting higher fungal activity on leaves. Bacterial communities on leaves were also significantly affected. Similarly, increases in net primary production, sediment microbial respiration and chlorophyll a content on the sediment surface were greatest in the channels receiving a fungal inoculum. These results point to a major role of fungal communities in stream ecosystems beyond the well-established direct involvement in leaf litter decomposition.