The mountains of Kyrgyzstan are geologically young, so that the physical terrain is marked by sharply uplifted peaks separated by deep valleys (see fig. 9). There is also considerable glaciation. Kyrgyzstan's 6,500 distinct glaciers are estimated to hold about 650 billion cubic meters of water. Only around the Chu, Talas, and Fergana valleys is there relatively flat land suitable for large-scale agriculture.

Because the high peaks function as moisture catchers, Kyrgyzstan is relatively well watered by the streams that descend from them. None of the rivers of Kyrgyzstan are navigable, however. The majority are small, rapid, runoff streams. Most of Kyrgyzstan's rivers are tributaries of the Syrdariya, which has its headwaters in the western Tian Shan along the Chinese border. Another large runoff system forms the Chu River, which arises in northern Kyrgyzstan, then flows northwest and disappears into the deserts of southern Kazakstan. Ysyk-Köl is the second largest body of water in Central Asia, after the Aral Sea, but the saline lake has been shrinking steadily, and its mineral content has been rising gradually. Kyrgyzstan has a total of about 2,000 lakes with a total surface area of 7,000 square kilometers, mostly located at altitudes of 3,000 to 4,000 meters. Only the largest three, however, occupy more than 500 square kilometers. The second- and third-largest lakes, Songköl and Chatyr-Köl (the latter of which also is saline), are located in the Naryn Basin.