Navigation channels provide a vital link in the supply chain of inland transport. Excavation of sediment from the river bed and fluvial islands is necessary to make the large braided river navigable for transportation. Present research work investigates the feasibility of dredging operations in the mid-sand bars of the Brahmaputra River (Assam, India) for navigation purposes. Pernicious metal (Cu, Zn, Fe, Mn, Ni, Co, Cr, Pb, Cd) concentrations were assessed at 42 sampling locations, covering a reach length of approx. 600 km (reaches 1 and 2). Vertical samples were obtained from 0 cm, 50 cm, and 100 cm of the mid-sand bar. Various indices were evaluated to quantify the contamination level in the mid-sand bars. Based on the enrichment factor (EF), reach 2 was highly enriched with toxic metal-limiting dredging operation. Conversely, reach 1 was found suitable for dredging operations, owing to the low EF value. Various anthropogenic activities are likely to be the causative factor for the heavy metal enrichment in reach 2, including effluents from pharmaceutical industries, oil refineries, and industrial and domestic runoff. Statistical analysis also endorsed those heavy metals possess similar anthropogenic origins. Overall, the dredging can be feasible for reach 1 and at localized zones for reach 2 across the Brahmaputra River. Further, the study tries to present a suitable mitigation measure to carry out dredging operations and manage contaminated dredged sediment for reach 2.