The assessment of the carcinogenic risk of the impact of drinking surface waters on the population health of the transboundary basin of the Selenga river in Mongolia is described in the article. We carried out expeditionary studies of the quality of drinking surface waters on the territory of four aimags, which represent different degrees of economic development and are completely included in the Selenga river basin: Khuvsgul, Arkhangai, Bulgan and Selenge. In this work, we used the methodology used by the US Environmental Protection Agency to quantify the carcinogenic risk of exposure to chemical compounds present in surface waters using the example of these aimags in Mongolia. The application of this methodology for risk assessment gives a great advantage over traditional methods of regulation. It has been established that on the territory of the Selenge aimag, the risk of developing a carcinogenic effect from the impact of priority pollutants on public health associated with the quality of drinking water is high and in the territory of Bulgan, Khuvsgul and Arkhangai aimags are medium, which requires state regulation of the risk and the development of appropriate standards.