Hindukush (HK), Karakoram (KK), and Himalayan (HM) ranges (collectively called HKH), an extension of the Tibetan plateau, are sensitive areas for mercury (Hg) and other trace metals (TMs) contamination. These metals reach remote regions via long-range atmospheric transport from distant transboundary pollution sources, whereas local emissions, physiography, and climatic properties of alpine regions cause further enrichment of Hg and other TMs. Little is known about the chemical cycling of Hg and other TMs in the HKH region, which was investigated in the current study. Sediment and peat cores were taken from 10 remote lakes of the region, comprising three sediments and one peat core each from HM and KK, and two sediment cores from HK region. The mean concentration of total Hg in HM lakes was 13.08 µg/g, 8.46 µg/g in HK lakes, and 4.65 µg/g in KK lakes. Other metals, including iron (Fe), manganese (Mn), nickel (Ni), cobalt (Co), chromium (Cr), zinc (Zn), cadmium (Cd), arsenic (As), and selenium (Se), were also investigated in these cores. The mean concentrations of these metals in all three ranges were observed to be in decreasing order of Fe > Mn > Zn > Ni > Cr > As > Pb > Se > Cd. Overall, HM lakes were found to be highly enriched in Hg and other TMs, compared to KK and HK lakes. Both the mass burial rate (MBR) and mass burial flux (MBF) of Hg and other TMs were in decreasing order of HM > KK > HK. As a result of these findings, Hg might pose a potential risk within the remote lakes of HKH; therefore, further studies are highly recommended to understand the geochemistry, source apportionment, and bioaccumulation of Hg and other toxic metals in this pristine region.