Polychlorinated biphenyls (PCBs) are highly stable compounds in many aquatic environments, however they can be removed through the concerted activity of several bacterial groups under certain environmental conditions. The purpose of this study was to evaluate the responses of major bacterial groups in river sediments to several previously reported anaerobic PCB bioremediation treatments, including treatments with FeSO4, peptone, short-chain fatty acids, and incubation temperatures (10, 25, and 40°C). Clone libraries from sediments before exposure to anaerobic treatments were dominated by aerobic bacteria affiliated with beta-Proteobacteria, alpha-Proteobacteria, Sphingobacteria, and Nitrospira (44% of sequences) and anaerobic bacteria associated with delta-Proteobacteria and Chloroflexi (21% of sequences). Several significant changes occurred in the levels of these and other bacterial groups after exposing sediments to anaerobic treatments, including increased Firmicutes and decreased Proteobacteria, increased Bacteroidetes and decreased alpha-Proteobacteria at elevated temperatures, and increased Desulfitobacterium spp. in organic carbon-amended sediments. PCB dechlorination rates were also higher in the organic carbon-amended sediments. It is proposed that several bacterial groups identified in this study could serve as indicator taxa for assessing and optimizing PCB bioremediation conditions such as redox status and substrate availability in aquatic environments.