Heavy metal wastewater (HMW) has resulted in many adverse environmental issues. However, bioelectrochemical system (BES) has been recognized as an effective technology for HMW treatment. This technology generates electricity and removes heavy metals and high concentrations of sulfate. In the sulfate-reducing bacteria-based BES, sulfate-reducing bacteria can anaerobically reduce sulfate to produce sulfide, which reacts with heavy metal ions and forms their corresponding sulfide precipitates, or the heavy metals can be reduced by obtaining electrons at the anode or cathode of the BES. Therefore, this study comprehensively reviews the removal mechanisms of HMW at the anodes and cathodes of the BES. The effects of several key factors, such as electrode materials, biocathode, initial heavy metal concentration, external resistance, and pH, on electricity generation performance and removal efficiency were evaluated. Furthermore, the treatment effects of the microbial fuel cell-microbial electrolytic cell system and the coupled system of BES with plants, artificial wetlands, and electrolytic reactors on HMW and the recovery efficiencies of BES for sulfur and heavy (precious) metals were discussed. Therefore, this review provides a theoretical basis and technical support to broaden the prospects of BES application in HMW remediation.