From 1981 to 1985, comprehensive studies were conducted to develop the scientific rationale for establishing the reserve. In 2004, a new reserve was created in the central part of the Syrdarya Karatau, initially aimed at conserving and restoring the rare and endangered population of the endemic species listed in the International Red Book—the Karatau argali—and the local habitats of narrowly endemic plant species.
The Karatau State Nature Reserve was established to preserve the population of the Karatau argali and the local habitats of narrowly endemic plant species in the central part of the Syrdarya Karatau.

Flora
The Karatau Reserve has an exceptionally rich flora. On the mountain slopes and in the valleys, there are 1,600 species of plants, nearly a quarter of which are rare. The reserve is unparalleled in the country in terms of the number of endemic species. The Red Book includes 42 plant species. Here, one can find the semi-shrub tau-sagyz, which was discovered by scientists only in 1929. Additionally, the Karatau Reserve protects the populations of some of the rarest species, such as Tulipa turkestanica, Eremurus, Prangos, Cynoglossum, and wild tulips.

Fauna
Over the past 100 years, the composition of the fauna of the Karatau Reserve has changed significantly. Snow leopards and Tien Shan brown bears were completely exterminated in the mountains, and species such as roe deer, wild boars, and Tolai hares have become rare guests. Today, the main protected species are the Karatau argali, Indian porcupine, and stone marten. The mountain caves of Karatau have become home to several species of bats.

The Karatau Reserve is home to 118 species of birds. Among them are the white and black storks, vultures, snake eagles, dwarf eagles, saker falcons, steppe eagles, golden eagles, bearded vultures, beautiful cranes, lesser bustards, and owls. Notably, many of the nesting birds remain in the reserve for wintering. The rivers flowing from the southwestern spurs of the range host the Schizothorax intermedius fish.