Microorganisms play central roles in various processes in ecosystems, including biogeochemical cycling and the degradation of environmental contaminants. They may influence the water quality of aquatic ecosystems and some of them may serve as indicators of fecal pollution. As unique habitats that lie at the intersection of human activity and natural aquatic environments, man-made water features serve several important functions, including water storage and as transportation routes. In this chapter, we highlight recent advances in understanding the composition and function of microbial communities in various man-made water bodies, which will inform policies and tools that ensure the safe use of urban water resources.