The sources of the Kaidu River are located on the central southern slopes of the Tian Shan from where it flows through the Yulduz Basin and the Yanqi Basin into Lake Bosten for which it is the most important tributary. The river leaves the lake under the name Kongque River (), which literally means Peacock River, but is derived from the Uyghur name Konchi Darya which means Tanner's River. The Kongque River flows through the Iron Gate Pass () into the Tarim Basin.