► MFC utilizes DOMs in lake water for electricity generation. ► Protein-like substances were substantially degraded by MFC treatment. ► Genotoxic agents in polluted lake water were almost completely removed. ► A potential pretreatment technology for sustainable remediation of lake water. A microbial fuel cell (MFC) was explored as a pretreatment method to remove dissolved organic matter (DOM) from polluted lake water and simultaneously generate electricity. After the MFC treatment, the total organic carbon concentration in the raw lake water was reduced by 50%, the physicochemical nature of DOMs was substantially altered. Protein-like substances in lake water were utilized as a major substrate for the MFC, while humic-like substances were refractory to the biodegradation. A further investigation into the bovine serum albumin utilization in an MFC confirms that the electricity generation was closely associated with the removal of protein-like substrates. Toxicity assessment by Salmonella typhimurium Sal94 indicates that the genotoxic agents in the polluted lake water were almost completely removed after the MFC treatment. This approach of coupling microbially-catalyzed electricity generation with DOM removal may offer a potential avenue for energy-efficient bioremediation of lake water.