Persistent organic pollutants (POPs) and polycyclic aromatic hydrocarbons (PAHs) have previously been detected in the surface sediments, water, and endemic organisms of Lake Baikal, a UNESCO World Heritage Site. The Selenga River is the primary source of freshwater to Lake Baikal, and transports pollutants accumulating in the Selenga River basin to the lake. Sources of POPs and PAHs in the Selenga River basin grew through the 20th century. In the present study, temporal changes in the concentrations of PAHs and POPs were reconstructed from two lakes in the Selenga River basin over the past 150 years using paleolimnological techniques. Increased concentrations in PAHs and PCBs were recorded initially in the 1930s. The 1940s-1980s was the period of greatest exposure to organic contamination, and concentrations of dichlorodiphenyltrichloroethane (DDT), polychlorinated biphenyls (PCBs), hexachlorocyclohexanes (HCHs) and many PAHs peaked between the 1960s and 1980s in the two lakes. Declines in concentrations and fluxes were recorded for most PAHs and POPs in the 1980s and 1990s. Temporal trends in concentrations of total and individual compounds/congeners of PAH, PCBs, and polybrominated diphenyl ethers (PBDEs) indicate the contribution of both local and regional sources of contamination in the 20th and 21st centuries. Temporal variations in contaminants can be linked to economic and industrial growth in the former USSR after World War II and the economic decline of Russia in the late-1980s and early-1990s, as well as global trends in industrialization and development during the mid-20th century.