The Muzart River starts in the Muzart Glacier (木扎尔特冰川)[3] in the Tian Shan Mountains, not too far from the Khan Tengri Peak, and flows toward the southeast and east through Baicheng County, in the valley between the main range of the Tian Shan and the Queletage Mountains (却勒塔格山) to the south.

As the river flows east, toward Kucha, it crosses the Queletage Range in a steep valley.

[4] The river has been dammed at 41°44′45″N 82°26′40″E / 41.74583°N 82.44444°E / 41.74583; 82.44444, a short distance upstream of the Kizil site, forming a large man-made lake known as the Kizil Reservoir (simplified Chinese: 克孜尔水库; traditional Chinese: 克孜爾水庫; pinyin: Kèzī'ěr shuǐkù).

With the surface area of 50,000 m², the reservoir has been described as "the largest swimming pool" in southern Xinjiang.

[5] Farther east the river enters a wide plain, where most of its water is taken into irrigation channels supporting the agriculture of the Kuqa, Toksu, and Xayar Counties.