In arid regions, montane lakes are valuable water sources and play important ecological roles. However, recent human-induced inputs of organic pollutants are threatening lake ecology in such regions and becoming a matter of great concern. To investigate pollutant histories and sources, we measured polycyclic aromatic hydrocarbons (PAHs) and n-alkanes in a dated sediment core that spans the last ∼350 years, from montane Lake Issyk-Kul (Kyrgyzstan, Central Asia). Results showed that organic pollutants were delivered to Lake Issyk-Kul in four stages and that their concentrations increased from Stage I (∼1670–1800 CE) to Stage IV (∼2000–2010 CE). Furthermore, we tracked the sources of sedimented PAHs using their ratios combined with n-alkanes data. Ratios of PAHs Ant/(Ant + Phe), Flt/(Flt + Pyr) and Bap/BghiP indicated that inputs during Stage II (∼1800–1970 CE) and Stage III (∼1970–2000 CE) came mainly from high-temperature combustion of coal and vehicle emissions. PAHs in Stage I and Stage IV, however, were mainly derived from low-temperature combustion and petrogenic sources. Diagnostic PAH ratios, combined with the natural n-alkane ratio (NAR<0) and unresolved complex mixtures (UCM), showed that the sources of PAHs in Stage I were mainly from erosion of bedrock and partly influenced by forest wildfires, different from the source during Stage IV, which was mainly from refined petroleum caused by accidental spills. Our assessment of the contamination history of the lake indicates that toxicity risk to the waterbody from sediment PAHs is low, but recent discharges arising from traffic deserve attention.