Toxic and heavy metals cause direct and indirect damage to the environment and ultimately to humans. This study involved the isolation of indigenous bacteria from heavy metal-contaminated environments that have the ability to bioabsorb heavy metals such as cadmium, nickel, and lead. The bioabsorption process was optimized by varying parameters such as temperature, metal concentration, number of bacteria, pH, and more. The bacterial isolates were investigated in terms of morphology, biochemistry, and phylogeny, with 12 strains chosen in the initial stage and one strain chosen in the final stage. It should be remembered that the metal uptake capacity of all isolates was approximately calculated. A box and reactor were designed to house these optimized microorganisms. Based on biochemical, morphological, and molecular results, the isolated strain was found to be closely related to the Bacillus genus. In the first five steps of testing, the ideal pH for removing lead alone, lead with cadmium, lead with nickel, and lead ternary (with cadmium and nickel) by Bacillus bacteria was found to be 7, 6, 5.5, and 6.5, respectively. The absorption efficiencies for single lead (unary), lead together with nickel, cadmium (binary), and ternary (lead with cadmium and nickel) were found to be 0.36, 0.25, 0.22, and 0.21 mmol/g, respectively. The ideal temperature for lead removal was around 30 °C. The adsorption isotherm for each lead metal in different states was found to be similar to the Langmuir isotherm, indicating that the surface absorption process is a single-layer process. The kinetics of the process follow the second-order kinetic model. The amount of Bacillus bacteria biomass obtained during this process was approximately 1.5 g per liter.