The Altyn-Emel Biosphere Reserve is located in the central part of the Ili Inter-Mountain Basin. From a geobotanical and ecosystem perspective, the Kapchagay-Ili region holds special value as it is situated in the desert zone of Kazakhstan within an inter-mountain basin. This area is bounded to the west and north by the southern spurs of the Jungar Alatau, to the south by the Kapchagay Reservoir and the Ili River, and it features a rare combination of diverse landscapes and ecosystems within a relatively small area.

The ecosystem diversity comprises various zonal and intrazonal types, such as different types of deserts, riparian forests along the Ili River, deciduous and coniferous forests, salt marshes, and sedge meadows, among others. The unique vegetation of the Kapchagay Inter-Mountain Basin is determined by the physiogeographic features of the region against the backdrop of a sharply continental arid climate. Botanically and geographically, this area is located in the transitional zone between the Jungar and North Turan desert types, which explains the existence of unique plant communities and their combinations (Jungar, Jungar-North Turan, and North Turan).

Furthermore, the value of the Altyn-Emel Biosphere Reserve is justified by the presence of monuments and objects of historical and cultural heritage within its territory. The most significant among them are the “Singing Dune” nature monument of republican significance, the Katu Tau and Ak Tau Mountains, the Saka burial mounds of Bes-Shatyr, the Tanbaly Tas petroglyphs, and other objects.

Thus, the ecological significance of the Altyn-Emel Biosphere Reserve lies primarily in the preservation and reproduction of the unique animal and plant life, landscapes, and natural ecosystems of the Jungar Alatau Mountains and the Ili Basin. This also includes the most valuable water and wetland areas of the Ili River floodplain. The nature conservation regime and zoning of the reserve allow minimizing the harmful impact of human economic activities on protected ecosystems while actively promoting eco-tourism without causing harm. Overall, the natural environment and ecosystems are largely untouched by human activity.