The Yamuna River, a vital freshwater resource in northern India, has been subjected to severe contamination due to rapid urbanisation, industrial discharge, agricultural runoff, and cultural practices. This study examines the potential of bioremediation using indigenous microorganisms to remove heavy metals-specifically lead (Pb), cadmium (Cd), and chromium (Cr)-from the Yamuna River at Allahabad. Water, sediment, and fish tissue samples were collected from multiple sites along the river and analysed for heavy metal concentrations using Atomic Absorption Spectroscopy (AAS). In addition, histopathological evaluations were performed on tissues of Labeorohita to assess the biological impacts of chronic metal exposure. Indigenous bacterial isolates were obtained from contaminated sites and screened for their heavy metal tolerance. Laboratory-scale batch experiments were conducted to optimise parameters such as pH, temperature, and incubation time to maximise metal removal efficiency. The results indicated that heavy metal concentrations in water and sediments consistently exceeded national and international guidelines, and fish tissues exhibited significant bioaccumulation with corresponding histopathological damage. Notably, Pseudomonas aeruginosa and Bacillus subtilis strains demonstrated removal efficiencies of up to 85% for lead under optimised conditions. This study underscores the urgent need for integrated pollution control measures and highlights the potential of bioremediation as a sustainable, cost-effective alternative to conventional remediation techniques. The findings are intended to inform policymakers and environmental managers on strategies for river restoration, emphasizing the importance of strengthening regulatory frameworks, improving wastewater treatment infrastructure, and promoting public–private collaborations for effective river basin management.