The river rises on the north slopes of Kyrgyz Ala-Too and flows in north-north-east and north-east directions until confluence with its right tributary Tuyuk.

Then the river flows northward entering the Chüy Valley.

Ysyk-Ata is a left tributary of the Chu, the major watercourse of the valley.

Four lakes with an area of 0.5 square kilometres (0.19 sq mi) and some 70 glaciers with a total area of 71.8 square kilometres (27.7 sq mi) are located in the river basin.

Ysyk-Ata - a balneoclimatic resort is located at the river.