The article presents the results of the study of polychlorinated biphenyls (PCBs) pollution of water and bottom sediments of Markakol Lake and rivers of its basin. Brief information about the importance of studying the accumulation and distribution of these dangerous xenobiotics in water bodies and watercourses of the republic in order to realize the tasks adopted by the Republic of Kazakhstan in accordance with the requirements of the global Stockholm Convention on Persistent Organic Pollutants (POPs) is presented. The conducted research f irst of all showed pollution of water resources and bottom sediments of the lake and rivers located in the protected area. Uneven distribution of toxicant concentration over the lake water area both in water and bottom sediments was revealed. The highest toxicant concentrations were registered in the water of the Kalzhyr River outflowing from the lake. In lake and river waters, 30 individual PCB congeners were detected, among which highly toxic dioxin-like and «marker» congeners are present. Other congeners with rather high toxicity were also found in water resources. Based on the scientific results of scientists from far and near abroad in the field of problems of distribution of these toxicants on the planet, the hypothesis about atmospheric transfer of these toxic compounds to this protected zone from highly PCB polluted territories was made.