Streams present microorganisms with a unique set of physical and chemical conditions. The most apparent is the unidirectional flow of water. Streams also have strong interconnections to the surrounding landscape and are often exposed to extensive anthropogenic disturbance. This article is divided into three main sections: diversity and composition of microbial communities, biogeochemical functions, and anthropogenic impacts. In terms of diversity, high‐throughput sequencing has transformed microbial ecology; yet, streams and some taxa are relatively understudied. The dynamic nature of streams and large temporal and spatial differences also create challenges for development of generalities. The roles of microbes in organic matter processing and nutrient cycling in streams are clear, and the fate of nutrients has a large impact on downstream processes, such as eutrophication. Humans impact streams in a variety of ways that, in turn, alter the physiochemical conditions and microbial ecology. Often these impacts are combined, such as multiple pollutants in a channelized stream, making it difficult to discern the cause and effect. Overall, microbes are central to function of stream ecosystems biogeochemically. This coupled with the importance of streams to humanity makes the study of stream microbial ecology crucial. Molecular methods are at the heart of microbial ecology, and studies of streams also benefit from this approach.