The present study discusses the potentiality of using anaerobic Packed Bed Bioreactor (PBR) for the treatment of acid mine drainage (AMD). The multiple process parameters such as pH, hydraulic retention time (HRT), concentration of marine waste extract (MWE), total organic carbon (TOC) and sulfate were optimized together using Taguchi design. The order of influence of the parameters towards biological sulfate reduction was found to be pH > MWE > sulfate > HRT > TOC. At optimized conditions (pH - 7, 20% (v/v) MWE, 1500 mg/L sulfate, 48 h HRT and 2300 mg/L TOC), 98.3% and 95% sulfate at a rate of 769.7 mg/L/d. and 732.1 mg/L/d. was removed from the AMD collected from coal and metal mine, respectively. Efficiency of metal removal (Fe, Cu, Zn, Mg and Ni) was in the range of 94–98%. The levels of contaminants in the treated effluent were below the minimum permissible limits of industrial discharge as proposed by Bureau of Indian Standards (IS 2490:1981). The present study establishes the optimized conditions for PBR operation to completely remove sulfate and metal removal from AMD at high rate. The study also creates the future scope to develop an efficient treatment process for sulfate and metal-rich mine wastewater in a large scale.