The lake has been drying in the modern era, but that process has been stabilized by the construction of the Bukhtarma Hydroelectric Power Plant, of whose reservoir it's now a part.

During the Han-Xiongnu wars, Lake Zaysan and the Black Irtysh were a point of contention between the Chinese Han Dynasty and the Xiongnu, with a notable campaign made in the region by general Huo Qubing.

After the reformation of the nomadic state by the Gokturks in the 500s and their subsequent division into eastern and western halves, Lake Zaysan was conquered by China's Tang Dynasty in the 600s during the Battle of Irtysh River.

After the loss of the Tang's northern possessions, the lake came to be governed by various nomadic tribes of the Karluks and the Oirats during the middle medieval period from the 700s–1000s.

This prompted an increase in the Russian authorities' attention to their borderland; in 1756, the Orenburg Governor Ivan Neplyuyev even proposed the annexation of the Lake Zaysan region, but this project was forestalled by Chinese successes.

[12] Concerns were raised in Russia (1759) about the (theoretical) possibility of a Chinese fleet sailing from Lake Zaysan down the Irtysh and into Western Siberia.

Even though the Zaysan region was recognized by both parties as part of the Qing Empire, it had been annually used by fishing expeditions sent by the Siberian Cossack Host.

[15] The actual border line pursuant to the convention was drawn by the Protocol of Chuguchak (1864), leaving Lake Zaysan on the Russian side.

After the fall of the rebellion and the reconquest of Xinjiang by Zuo Zongtang, the border between the Russian and the Qing empires in the Irtysh basin was further slightly readjusted, in Russia's favor, by the Treaty of Saint Petersburg (1881).