The rising Tarbagatai Range split the fresh Zaysan and the brackish Alakol into independent lakes, causing them to significantly decrease in size.

Also during the Pleistocene, glaciations and intensive ice melting resulted in the Balkash deepening and increasing in size, reconnecting with the Alakol as a single lake.

By the Holocene, however, the area became shallow and the single body of water split up into modern lakes Balkhash, Alakol and Sasykkol.

Other important rivers are the Aksu, Koksu, Lepsy, Karatal, Emil, Urzhar, Tentek and Ayagöz, as well as the Tokrau and the Bakanas, which are part of the basin even though not reaching the lake.

The main species that grow are salt-tolerant shrubs and grasses, such as saxaul, Calligonum, saltwort, wormwood and winterfat.