This chapter investigates water pollution and the emerging role of different bioelectrochemical systems (BES) in the treatment of diverse classes of wastewater. Topics addressed include the source and composition of disparate wastewaters, their water contaminants, and conventional wastewater treatment methods. The different classes of BES and their electrically active microbial populations are discussed along with the mechanisms by which various pollutants are targeted, catabolized, precipitated, or otherwise remediated. The primary focus is on domestic and industrial wastewaters and treatment, although agricultural wastewater and stormwater runoff are also covered. Important water quality concepts like coliform indicator bacteria, BOD, TCD, and organic and inorganic pollutants are defined. This chapter concludes with an examination of newer BES technologies, such as photosynthetic microbial fuel cells, and the technical and economic challenges and opportunities related to the future implementation of BES at wastewater treatment facilities.