The objective of the current study was to assess the contamination of potentially toxic metals (PTMs) in weathered surface sediment, along stream tributaries, and surrounding area of the river Chitral, Shyok suture zone district Chitral, Pakistan. To understand the geochemical features of 113 sediment, samples were collected from the Mirkhani and Drosh area. Then, different statistical tools including the geo-accumulation index (Igeo), cluster analysis (CA), principal component analysis (PCA), and ecological risk assessment (ERA) were used to unravel the origin, intensity, and exposure level of PTMs to control risk and restore the ecosystem within the study area. The results for the PTMs namely nickle (Ni), chromium (Cr), copper (Cu), cadmium (Cd), lead (Pb), zinc (Zn), and cobalt (Co) in Mirkhani and Drosh were in the following ranges: 10–150, 15–210, 15–250, 0.08–1.00, 10–70, 76–240 and 14–51; and 13–240, 17–210, 15–150, 0.08–0.60, 7–140, 47–150 and 13–36 mg/kg, respectively. In consequence, the potential ecological risk caused by Pb, Ni, Cu, Co, Cr, and Zn is reflected by the percentages of samples with an ecological risk index (ERI) greater than one which were 100%, 91%, 100%, 100%, 92%, and 100%, respectively. However, the overall mean decreasing order of ecological risk of PTMs in the district Chitral was Pb > Ni > Cu > Co > Cr > Zn > Cd. Moreover, the PCA yielded 78% variability which indicated that mineral prospects play an important role in the contamination of sediment. Furthermore, the mineral phases of Pb and Zn suggested supersaturation, while that for Cd revealed unsaturation. The results of Igeo, ERI, and CA indicated contamination of PTMs in the study area. The ERI value of Pb, Ni, Cu, Co, Cr, and Zn was higher than 1 suggesting an ecological risk in the study area. Moreover, the current study showed the dominance of geogenic contamination with major contributions from ultramafic rock and known mineral prospects. Therefore, contaminated sediment of the Shyok suture zone is extremely detrimental to the aquatic ecosystem of the study area.