Microplastic (MP) pollution is a critical environmental challenge worldwide, however limited research is reported in remote lakes of Pakistan. This study assessed MPs (>5mm) prevalence, distribution and risk perspective in water and sediment of eight remote and high-altitude lakes (> 1,500 meter above sea level) of Gilgit Baltistan, Pakistan. The lakes exhibited an average abundance of 152.6 ± 104.6 to 12.1±7 MPs/kg of dry sediments and 2 ± 0.9 to 17.1 ± 17.2 MPs/L of surface water. MPs <200μm dominated in both matrices. Surface water predominantly contained polyester and polypropylene, while polypropylene and polyethylene dominated in sediments. The gradient of elevation did not show any pronounced impact on the fiber loading or MP count in both matrices. Backward air mass trajectory revealed that air masses vastly travelled from western-Asia, Arabian sea and Bay of Bengal with an average transmission distance of 2,500-3,500 km (500 m a.s.l) that can be a potential deposition MP source in the area. Pollution Load Index of the lakes were >1 exhibiting pollution. All other lakes except Batura and Borith manifested a moderate hazard index. Naltar lake along with aforementioned two lakes also manifested high polymer toxicity. Further research should emphasize understanding the mechanisms and biotic interactions in high-mountain ecosystems.