This paper investigates the removal of iron and zinc from aqueous solution with daily wastewater in three different biomasses such as Lactobacillus delbrueckii ssp bulgaricus (Lb-12), Streptococcus thermophillus (STM-7) and a combination of both this bacteria culture (YC-380) and the optimization of removal efficiency using MINITAB program. A full 2(3) factorial design of experiments was applied to determine the optimum conditions of removal of Fe(II) and Zn(II) from aqueous solution. The three tested factors were biomass concentration (5-15 g/L), pH (3-9), and temperature (20-40 degrees C). The optimum biomass concentration, pH and temperature were found to be 15 g/L, 9 and 20 degrees C, respectively. Under optimal value of process parameters, 90-100% Fe(II) and 70-90% Zn(II) removal were obtained with all tested biomasses. Removal results indicated that a combination of both this bacteria might be a promising biomass alternative to ST-M7 and Lb.12 in removing Zn(II) and Fe(II) ions from waters.