<p>Atmospheric deposition of persistent toxic substances represents a potential threat to pristine mountain ecosystems, where precipitation and meltwater from snow and glaciers are essential components of downstream water supply. We investigated the concentrations of polycyclic aromatic hydrocarbons (PAHs) in surface waters of the western Tianshan Mountains in Kyrgyzstan, and used <i>n</i>-alkane and water isotope values (δD and δ¹⁸O) to elucidate PAH sources and the factors that influence their distributions. PAH concentrations in lake and river waters were 21.00 − 68.05 ng L^–1 and 13.84 − 81.57 ng L^–1, respectively, with high fractions of low-molecular-weight (LMW) compounds. Based on <i>n</i>-alkane profiles and a positive matrix factorization (PMF) model, we determined that PAHs in the study area originated from biomass combustion (42.8%), petroleum input (23.6%), vehicle emissions (16.3%) and coal burning (17.3%). Highly contaminated sites, with greater abundance of heavy compounds and higher stable isotope values, were closer to large settlements, indicating contributions from local human impacts on the PAH loads in waters. Elevated LMW-PAH concentrations in river waters with more negative isotope values, and altitude-dependence of LMW congeners, indicated that atmospheric deposition is responsible for the spatial distribution of more volatile PAHs. Risk estimation suggests possible effects of PAHs on ecosystem biota, but negligible non-carcinogenic and carcinogenic effects on humans, from either dermal contact or water ingestion.</p>