According to the botanical and geographical zoning, the territory of the reserve is part of the Sahara-Gobi desert region, the Iran-Turan subdistrict, the North Turan province, and the Central North Turan subprovincion.

The territory of the reserve is located in the subzone of medium-sized real deserts.

The vegetation cover of the reserve is divided into vegetation of the modern and ancient delta of the river. Silt and vegetation of the abrasive-accumulative plain of the southern coast of Lake Balkhash.

The vegetation of the reserve is represented by five types: tugai, meadow, swamp, submerged, and desert.