The Nkusi River begins in the hills west of the town of kakumiro in the kakumiro district. It flows in a north-westerly direction to enter a swamp near the village of kitoma, in the Kibaale district. The river emerges from this swamp and flows westwards to empty into Lake Albert at the border with the Democratic Republic of the Congo.

In the swamp near kitoma, the Nkusi River briefly joins the river kafu. The river kafu, however, flows out of the swamp in a north-easterly direction and finally empties into the Victoria Nile, near the town of Masindi port in Masindi district.

The source of the Nkusi River is in kakumiro the river enters Lake Albert at kigwabya in Kibaale district at its source, the altitude is approximately 1,334 meters (4,377 ft) at its point of entry into Lake Albert, the altitude is approximately 616 meters (2,021 ft ) the length of the river is approximately 160 kilometers (99 mi)