Thereafter it cuts across an offshoot of the Karakoram range and flows in a southerly direction before it is joined by the Ghizar River flowing in from the west. The Gilgit River then flows eastwards and merges with the Indus at Bunji just before the latter river has cut a path through the main Himalayan range.

The entire catchment area of the Gilgit River is bleak and desolate. Vegetative growth is extremely poor and consists of low forms of plant life occurring along water channels from spring to autumn each year. Bunji is the main human settlement along this river.