The article presents the results of an analysis conducted by the State Enterprise Central Laboratory under the Ministry of Natural Resources, Ecology, and Technical Supervision of the Kyrgyz Republic, focusing on the concentrations of major ions, heavy metals, and nitrogen in water samples collected from the Zhyrgalan River basin within the Issyk-Kul basin, the country’s main sanatorium and resort region. The study indicates that the concentrations of major ions in the waters of the Zhyrgalan River basin are within the permissible limits established by maximum permissible concentrations (MPC). However, elevated levels of certain heavy metals were detected in all samples, exceeding the standards set by the Law of the Kyrgyz Republic “Technical Regulations on the Safety of Drinking Water” (as amended on April 28, 2017). Increased concentrations of these metals deteriorate the drinking water quality and may cause serious adverse effects on human health. The analysis of the chemical composition of the Zhyrgalan River waters in the Issyk-Kul basin demonstrates that, for their use in drinking and domestic purposes, priority measures should focus on the removal of heavy metals. Continued systematic monitoring of river water quality in the Issyk-Kul basin, with particular emphasis on heavy metal determination, is therefore recommended.