Hexavalent chromium (Cr (VI)) and para-chlorophenol (4-CP) are prevalent industrial wastewater contaminants that are recalcitrant to natural degradation and prone to migration in aquatic systems, thereby harming biological health and destabilizing ecosystems. Consequently, their removal is imperative. Compared to conventional chemical treatment methods, CW-MFC technology offers broader application potential. Leersia hexandra Swartz can enhance Cr (VI) and 4-CP absorption, thereby improving wastewater purification and electricity generation in CW-MFC systems. In this study, three CW-MFC reactors were designed with L. hexandra Swartz in distinct configurations, namely, stacked, multistage, and modular, to optimize the removal of Cr (VI) and 4-CP. By evaluating wastewater purification, electrochemical performance, and plant growth, the optimal influent hydraulic retention time (HRT) was determined. The results indicated that the modular configuration at an HRT of 5 days achieved superior removal rates and power generation. The modular configuration also supported the best growth of L. hexandra, with optimal photosynthetic parameters, and physiological and biochemical responses. These results underscore the potential of modular CW-MFC technology for effective detoxification of complex wastewater mixtures while concurrently generating electricity. Further research could significantly advance wastewater treatment and sustainable energy production, addressing water pollution, restoring aquatic ecosystems, and mitigating the hazards posed by Cr (VI) and 4-CP to water and human health.