Microbes play numerous roles in stream ecosystems. They carry out key processes in stream nutrient cycles and are responsible for a large part of organic matter breakdown. Advances over the past 25 y in our understanding of which microbes are linked to specific processes have been rapid and fundamental, in part, because of improvements in methods. It is now clear that immobilization of inorganic nutrients and other transformations are just as important as release of nutrients during organic matter decomposition. Microbial biomass is recognized as a key portion of trophic transfer, but our understanding of the pathways of connection have changed. Information on the actual composition of microbial communities is very recent, and it is still unclear whether there are consistent biogeographic patterns in freshwater bacterial composition. One of the major areas of potential advancement is clarifying the linkage between microbial community composition and ecosystem function. Determining the strength of the connection between microbial assemblage composition and the processes they catalyze remains a technical and conceptual hurdle. Quantifying the strength of this linkage seems necessary to understand variability in both composition and function because feedbacks are likely in cases where the link is strong. The future of the field is bright, but we need to understand how microbes and the processes they carry out will respond to climate change and novel stream management approaches.