The regions of Bolkar Mountains and Aladağlar accommodate a unique ecosystem in Turkey, due to being in a transitional climate between the continental and the Mediterranean and hosting alpine lakes which are considered as good indicators of regional and atmospheric pollution due to being far from direct human impact. On the other hand, these regions are surrounded by various power plants, and also subject to occasional human activities, where anthropogenic effects are expected to be. Sediment samples were collected from 12 lakes in Central Taurus Mountains, 6 lakes in Bolkar Mountains, and 6 lakes in Aladağlar. Fifteen PAHs, identified as priority pollutants by the US Environmental Protection Agency (EPA), as well as lake water chemical characteristics were determined. The distribution of analyzed PAHs was investigated, and PAH diagnostic ratios were calculated to identify their potential sources. It was a remarkable observation that only low-molecular-weight PAHs exist in the lakes of Aladağlar, whereas high-molecular-weight PAHs are also found in the lakes of Bolkar Mountains, likely reflecting more isolated characteristics of the Aladağlar region. As compatible with this observation, total PAHs (T-PAHs) were found lower in Aladağlar (0.00–105.78 ng/g w.w.) than in Bolkar Mountains (9.08–380.16 ng/g w.w.). Overall, T-PAHs of sampled lakes were found in a similar range when they are compared to the other high-altitude alpine lakes around the world, indicating no significant difference in terms of atmospheric pollution of the global average.