Heavy metal contamination represents a critical environmental and public health challenge, necessitating effective remediation approaches. This study examines the bioremediation potential of three indigenous bacterial strains Aeromonas caviae KQ_21, Aeromonas hydrophila AUoR_24, and Shewanella putrefaciens SUoR_24 evaluated both individually and in consortia for their capacity to remove heavy metals. Tolerance assessments demonstrated that the coculture of these strains exhibited superior resistance to copper (Cu), zinc (Zn), and nickel (Ni), with optimal growth observed up to 6 mM for Cu, 9 mM for Zn, and 5 mM for Ni, outperforming the monocultures. The co-culture system also achieved higher metal reduction efficiencies, with reductions of 47.02% for Cu, 61.49% for Ni, and 61.93% for Zn, in contrast to lower reductions observed in individual strains. The study further explored the impact of environmental conditions on bioremediation efficiency. Optimal temperature for both monoculture and coculture setups was found to be 30 °C. pH and salt concentration variations significantly affected bacterial growth and metal reduction, highlighting the necessity of tailored conditions for enhanced bioremediation. In terms of metal removal mechanisms, the results demonstrated that nickel (Ni) removal occurred primarily through bioaccumulation, while copper (Cu) removal involved both biosorption and bioaccumulation. Zinc (Zn) removal was facilitated through biosorption, bioaccumulation, and biotransformation. These findings underscore the effectiveness of bacterial consortia, particularly indigenous strains, in improving heavy metal tolerance and reduction through synergistic interactions and cooperative metabolic processes. This research offers valuable insights into optimizing bacterial consortia for environmental cleanup and advances the application of indigenous bacteria in bioremediation strategies. Future investigations should focus on exploring additional microbial species and further elucidating the molecular mechanisms that contribute to enhanced bioremediation efficacy.