Microbial communities associated with leaf litter in streams provide key ecosystem services through the cycling of energy and nutrients that can be influenced by environmental factors. We examined the effects of land use on leaf-litter microbial communities in boreal streams by comparing the structural (i.e. fungal and bacterial biomass and community composition by next generation sequencing) and functional (i.e. decomposition, and extracellular enzyme activities) characteristics of the microbial communities. Streams draining watersheds with histories of fire, logging, industrial-mining and urban watershed activity were compared to reference streams. The most severely disturbed industrial and industrial-urban streams had the lowest rates of microbial litter decomposition, greatly decreased fungal biomass and lacked the ubiquitous bacterial genera Pseudomonas, and Amantichitinum. Hydrolase activity was lowered in all streams with a history of disturbance, with potential adverse effects on energy and nutrient cycling. Our findings demonstrate that the microbial cycling of energy and nutrients in the boreal aquatic ecosystem is affected by land-use disturbance and illustrate the excellent potential of using microbial communities to track the effects of watershed disturbance and restoration efforts on boreal shield aquatic ecosystems.