The Yamuna River, a crucial freshwater resource in northern India, has been severely impacted by rapid urbanisation, industrialisation, agricultural runoff, and cultural practices, leading to elevated levels of heavy metals. This study examines the bioaccumulation of heavy metals-specifically lead (Pb), cadmium (Cd), and chromium (Cr)-in aquatic organisms, focusing on Labeorohita collected from the Yamuna River at Allahabad. Water, sediment, and fish tissue samples were analysed using standard methods, including Atomic Absorption Spectroscopy (AAS) for metal quantification and histopathological techniques for tissue evaluation. The results indicate that heavy metal concentrations in water and sediments frequently exceed national and international safety standards. Additionally, fish tissues demonstrated significant bioaccumulation of these toxic metals, with histological alterations such as gill lamellar fusion, hepatic vacuolation, and renal tubular degeneration. Seasonal variations were observed, with higher pollutant concentrations during the pre-monsoon period when dilution is minimal. Indigenous bacterial isolates were also tested for their potential in bioremediation, showing promising removal efficiencies. The study underscores the need for stringent pollution control measures, effective wastewater treatment, and integrated river basin management to mitigate the adverse impacts on aquatic life and human health. The findings provide critical insights for policymakers and stakeholders aiming to restore the ecological balance of the Yamuna River.