A series of mountain chains that are part of the Tian-Shan system, including the Alatau ranges, spur off into Kyrgyzstan . Most of these ranges run generally east to west, but the Fergana Mountains in the central portion of the country run southeast to northwest. The Fergana Valley in the west and the Chu Valley in the north are among the few significant lowland areas in Kyrgyzstan . The Naryn River, Kyrgyzstan's largest river, originates in the mountains in the northeast and flows westward through the middle of the country. The Naryn then enters the Fergana Valley and crosses into Uzbekistan , where it joins with another river to form the Syr Darya , one of Central Asia 's principal rivers. The Chu River , in northern Kyrgyzstan , flows northward into southern Kazakhstan . Yssyk-Kul, the largest lake in Kyrgyzstan and one of the largest mountain lakes in the world, is located at an altitude of 1,607 m above sea level in the northeastern portion of the country.

Forests occupy 4 percent of the country's land area. Coniferous trees such as the Tian-Shan white spruce grow along lower valleys and on north-facing mountain slopes. Many rare animal species inhabit the woodlands, including the Tian-Shan bear, the red wolf, and the snow leopard, which are protected by government decree. Other animals in Kyrgyzstan include deer, mountain goats, and mountain sheep. Kyrgyzstan 's mountain lakes are an annual refuge for thousands of migrating birds, including the mountain goose and other rare species.

Kyrgyzstan 's natural resources include significant deposits of gold and other minerals. Also present are deposits of coal, uranium, mercury, antimony, nepheline, bismuth, lead, and zinc. Exploitable but small reserves of oil and natural gas also exist. The country's fast-flowing rivers provide hydroelectric power. Only 7 percent of the total land area is cultivated.

The country's climate varies by region. The climate is subtropical in the Fergana Valley and temperate in the northern foothill zone. The lower mountain slopes have a dry continental climate, as they receive desert-warmed winds from Kazakhstan and Uzbekistan , whereas the highest mountain elevations have a polar climate.