The levels of heavy metals were determined in the river and drinking waters of the localities of the Ton and Jety-Oguz Districts of the Issyk-Kul Region of Kyrgyzstan. The quality of water was tested for the content of 11 heavy metals (Be, Pb, Cd, Ni, Co, Cr6+, Zn, Ba, Sr, Tl, Sn) by emission spectral analysis in 1990-2000. The analysis of the findings indicated that the water levels of the heavy metals met the sanitary requirements for drinking water, except for those of chromium whose content in the Barskoon and Chon-Kyzyl-Suu rivers in the cold period of 1999 was 2-3 times higher than the allowable levels. There were seasonal variations in the concentrations of heavy metals in the river waters. In most cases, the concentrations of most metals increase in the warm period of a year. The concentrations of heavy metals tended to increase in the river water in 2000 versus 1999.