We quantified polycyclic aromatic hydrocarbons (PAHs) and heavy metals (HMs) in the sediments and aerosols of the Eastern Himalayan Lakes, collected over four years from three high altitude Lakes (HALs), i.e., Sungester Lake, P.T. Tso Lake, and Sela Lake. The focus was to carry out source apportionment using multivariate statistical analyses. PAH concentrations (∑PAHs) in the core sediment during the pre-monsoon were higher than the post-monsoon, suggesting an elevated sedimentation rate in the lakes. In general, low molecular weight PAHs (LMWPAHs) were more abundant than high molecular weight PAHs (HMWPAHs) in both pre-and post-monsoon seasons in surface and core sediment samples. The 4-ring PAHs were the most profuse among all samples, followed by the 5-ring, 3-ring, and 2ring PAHs. The average diagnostic ratio indicated that PAHs sourced from pyrogenic coal combustion, fossil fuel and diesel emissions. Metal fractionation revealed the predominant presence of Fe in all the HALs, with the highest concentration in Lake P.T. Tso. The residual fraction was highest for all HMs, except Cd, where the exchangeable fraction was prominent. HYSPLIT model implied that long-range transported atmospheric pollution from the mid-Gangetic plains significantly impacts the sediment of lakes in the region.