The objective of this present study is the optimization of process parameters for the biosorption of Cr(VI) and Cu(II) ions by Bacillus subtilis in a packed bed bioreactor using response surface methodology (RSM). Continuous biosorption studies were conducted under optimized bed height, initial metal ions concentration, and flow rate for the removal of Cr(VI) and Cu(II) ions using B. subtilis. The biosorption parameters were optimized using RSM in both batch and packed bed bioreactor studies. From the studies it is noticed that the maximum biosorption of Cr(VI) and Cu(II) by B. subtilis was at optimum conditions of contact time of 30min, pH of 4.0, biomass concentration of 2mg/mL, and temperature of 32 degrees C in batch biosorption studies and bed height of 20cm, flown rate of 300mL/h, and initial metal ion concentration of 100mg/L in packed bed bioreactor biosorption studies. Predicted percent biosorption of the selected heavy metal ions by the design expert software is in agreement with experimental results of percent biosorption. The percent biosorption of Cr(VI) and Cu(II) in batch studies is 80 and 78.4%, respectively. The percent biosorption of Cr(VI) and Cu(II) in packed bed bioreactor studies is 91.7 and 94%, respectively.