Gilgit River Basin (GRB) is one of the primary fluvial aquatic systems flowing through Gilgit-Baltistan and a water source for recreation, fisheries, irrigation, and drinking to more than 1.8 million people. This study aimed to investigate heavy metals (HM) contamination levels in sediments of GRB, northern Pakistan. Fifty-five samples were picked from the various sections of GRB and examined for HM concentrations. Fe showed the maximum average concentration of 27,743 mg/kg, while Cd was noted with a minimum average of 1.06 mg/kg. HM concentrations were noted within the world river system guidelines except Cd, which also surpassed the sediment quality guidelines set by USEPA. HM concentrations of GRB sediments were used for the geospatial and ecotoxicological risk indices. Geospatial analyses showed higher levels of HM contamination and risk in the sediments of Ishkomen River in GRB. HM contamination in GRB sediments showed low to moderate levels of risk to exposed aquatic ecosystems. Statistical analyses were used for the HM source apportionment in sediments of GRB, suggesting a major contribution from natural activities. This study recommends seasonal variation in HM contamination of water and sediments studies in the GRB.