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This study focuses on heavy metals distribution and their ecological risk in river water, bed sediment, and suspended particulate matter (SPM) along the Ganga River basin. Overall abundance of the metals followed the sequence, Fe > Al > Mn > Pb > Ni > Cd > Cr > Zn > Co in water, Al > Fe > Mn > Zn > Cr > Cu > Ni > Co > Pb > Cd in bed sediment, while Al > Fe > Mn > Cr > Zn > Ni > Cu > Pb > Co > Cd in SPM. Among the abundant metals, Fe and Mn average concentrations exceeded BIS and WHO limits in river water. Similarly, Fe, Cd, and Zn, and most metals exceeded local background concentrations in bed sediment and SPM, respectively. Major ion chemistry in water signified carbonate weathering dominance during the time of sampling. Generally, Mn, Ni, Cu, Cr, and Co were derived from natural weathering and erosion, while Zn, Cd, and Pb were derived from both natural and anthropogenic sources. Metal index (MI) for river water showed that 27% of the locations were anthropogenically affected, whereas contamination factor and ecological risk assessment indicated highest contamination and risk from Cr and Cd in suspended sediments around urban centers in the middle basin. Furthermore, the confluence of Chambal and Yamuna increased heavy metal load in Yamuna and Ganga, respectively. The study highlighted the role of the water–sediment interaction indicating SPM is acting as a sink for metals followed by bed sediment.