According to the study of its 3,000 m-thick lake deposits, Lake Issyk-Kool (Issyk Kul) was born 20 million years ago in early Miocene, when an isolated intermountain depression was formed by intensive tectonic movements and was filled with water. The freshwater lake which existed in Pliocene was larger than the present lake.

Currently, Issyk-Kool is located at an altitude of 1,606 m (in 1990) in an oval-shaped basin surrounded by steep slopes on its periphery. The catchment area measures 252 km x 146 km and is bordered by high mountain ridges reaching 4,000 5,200 m in altitude on both the northern and the southern side. There are 834 glaciers on the alpine slopes of the basin, which supplies water of about 48x1.0E+9 m3 annually. In accordance with the gradient of climatic aridity, different landscape types, desert, semi-desert and steppe from west to east, alternates on the flat part of the catchment (exceeding 3,000 km2).

The basin of the lake itself has a rather simple shape like a truncated cone inverted. The lower base of the cone, 1,357 km2 wide, is almost flat ranging between 600 m and 668 m in depth. The shelf zone down to 300 m depth consists of several old terraces indented by 40 50 m deep canyons. Issyk-Kool never freezes even in severe winters. Water temperature does not fall below the temperature of maximum density (2.75 deg C at the mineral concentration of 6 ) except in shallow inlets.

The coastal zone of the Issyk-Kool has undergone continuous changes due to the gradual sinking of the lake water level during the present century (at a rate of about -5 cm yr-1). Shoals have dried up, and bars, spits, islands and littoral banks have newly appeared. The area already dried up during the last 25 years amounted to more than 55 km2.

The interaction of east and west winds, which often act simultaneously within the catchment basin, creates a cyclonic vortex with its divergence zone at the lake center and the convergence zone in the lake's periphery, causing the upwelling of cool deep water in the central part of the lake as well as the sinking of warm surface water in the sublittoral zone. As the result, the lake accumulates a large amount of heat during the warm season. Every fourth day is stormy on Issyk-Kool, and this explains the occurrence of a dome of cool water at the lake center, the prevalence of cyclonic current system and the absence of freezing. This dynamics of the lake water causes another feature an extremely high transparency at the center of the dome. Secchi disc reading reached 53 m in that very place in the stormy winter of 1985 (Q, 1, 2, 3, 4, 5).