Objective: To investigate the biosorption potential of isolated bacteria as an alternative biosorbent material for the removal of zinc and nickel from aqueous solution in a bubble column bioreactor. Methords: In this study from four points of waste water treatment plant, some Gram-positive and Gram-negative bacteria under heavy metal stress conditions were isolated by microbiological methods. Biosorption experiments were conducted in a bubble column containing waste water in high concentrations of nickel and zinc inoculated by isolated bacteria. A kinetic study was done to investigate the fitting of either pseudo first-order or second order equations. Results: The 96% removal of zinc and 54% removal of nickel were achieved by biosorption column experiment by the isolated bacteria. A comparison between a non-aerated and aerated column shows a higher removal percentage with the same contact time. The study of contact time in the experiments also confirmed that with more contact time, while the removal efficiency increases the capacity of microorganisms to absorb the metal ions decreases. Results of kinetic study showed pseudo-second-order equation with a coefficient of determination of 0.9648 and 0.9992 for zinc and nickel, and the pseudo-first-order equation with 0.2410 and 0.4794, respectively. Conclusions: It was be concluded that biosorbtion method is a suitable alternative method to remove metal ions for further study in large scale.