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Lake ecosystems in northern Pakistan are the most critical resources that maintain and regulate water flow for downstream agricultural, domestic, industrial, and ecological processes. One consequence of these processes is that ecosystems deposit heavy metals (HMs), where lake stagnant conditions result in high vulnerability of water resources. For this purpose, the present study examined HMs such as cadmium (Cd), chromium (Cr), cobalt (Co), iron (Fe), manganese (Mn), nickel (Ni), lead (Pb), and zinc (Zn) concentrations in high-altitude lakes (HAL) sediments of Mansehra district, northern Pakistan. Sediment samples were collected from the five HAL. This study used HM concentrations in lake sediments for the pollution factors such as contamination factor (C f ), pollution load index (PLI), sediment pollution index (SPI), ecological risk assessment (ERA), and risk index (RI). Among HMs, Fe showed the uppermost levels of 1410 mg/kg in lake sediment, while Cd with lowermost levels of 1.05 mg/kg. Results revealed that most HM concentrations in HAL sediments were within the threshold of sediments quality guidelines (SQGs), except for Cd. Among lakes, the sediments of Siri Lake showed higher contamination of HMs than others. Siri Lake sediments also showed higher C f , PLI, ERA, and RI values than others. The majority of HMs in HAL sediments showed no contamination, except for Cd (considerable) and Pb (moderate) levels to the exposed aquatic ecosystem. This study revealed that 95% of sediment samples in HAL were noted low to medium-level risks to the exposed aquatic communities. Statistical and geospatial analyses revealed that geogenic sources of contamination are a significant contributor to HM contamination of HAL sediments compared to others., Competing Interests: Declarations Ethics approval Not applicable. Consent to participate All authors reviewed and approved the final manuscript. Consent for publication All authors are approved for this publication. Conflict of interest The authors declare no competing interests., (© 2024. The Author(s), under exclusive licence to Springer Nature Switzerland AG.)