The entire district may be regarded as the basin of the Tawang Chu river.

In addition, two south-flowing rivers from Tibet, viz., the Tsona Chu and Nyamjang Chu, join the river within the district.

The combined river flows west into Bhutan, where it progresses to the Manas River (tributary of Brahmaputra River) and flows into the Assam state of India.

After Tsona Chu joins it, near Kyelatongbo at an elevation of 2,240 metres (7,350 ft), the combined river is called Tawang Chu.

The river flows west towards Bhutan, passing by the Tawang town on its southern flank.