Sediments are a sink and source for potentially toxic elements (PTE) contamination in aquatic systems. Among aquatic systems, lakes ecosystem play a significant role in managing, maintaining, and supplying water for several environmental and ecological services. The lake has a slow rate of water inflowing contaminant circulation, building up higher contaminants and hence making it most vulnerable. This study focused on and explored the sediments for PTE concentrations in the high-altitude lakes ecosystem of Swat Valley, northern Pakistan. The sediment samples were collected and analyzed for PTE concentrations. Among PTE, iron (Fe) showed an uppermost level of 1024 ± 94.2 mg/kg in Izmis Lake sediments, while cadmium (Cd) noted with a lowermost of 0.30 ± 0.1 mg/kg in Kandol Lake. PTE concentrations in the high-altitude lakes were noted to be lower than the sediment quality guidelines (SQGs), except for copper (Cu) and cadmium (Cd). The concentrations of PTE were utilized to calculate pollution factors and ecotoxicological risks. The contamination factor (Cf) of sediments in high-altitude lakes observed low to moderate contamination levels and ecotoxicological risks. Among high-altitude lakes, the Izmis Lake showed maximum Cf, pollution load index, and risk values for most of PTE than others. Statistical analyses revealed a significant correlation for most PTE and noted geogenic sources of contamination in sediments of high-altitude lakes.