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Abstract The present work focuses on biodegradation of naphthalene by using batch moving bed bioreactor (MBBR) with mixed microbial consortia maintained in anaerobic, anoxic, and aerobic conditions. All the three reactors were exposed to 10 to 100 mg/L of naphthalene. An acclimatized microbial consortium was able to degrade the naphthalene nearly 90% to 94.8% and remove 76% to 91% chemical oxygen demand (COD) in anaerobic, anoxic, and aerobic reactors at 24 hours retention time (RT). Response surface methodology (RSM) was used for the optimization of process parameters using Design Expert 10 software. The optimum process parameters predicted by RSM for 100 mg/L influent naphthalene concentration is 18 hours RT to achieve 94.69% and 99.04% removal in anaerobic and aerobic reactor, whereas the optimum RT is found as 8 hours in anoxic reactor with 95.67% naphthalene removal. The design of experiment by RSM suggests that quadratic model can be best fitted to the present experimental study.