The Nossob has its origin in two main tributaries, the Swart-Nossob and Wit-Nossob, meaning black and white respectively. Both tributaries have their origins in the eastern slopes of the Otjihavera mountain range, east of Windhoek. Their sources are at 1,800 m and over 2,000 m above sea level respectively. The two river beds have their confluence some 80 km south of Gobabis, which is situated on the bank of the Swart-Nossob.
From this confluence the river course passes the settlements of Leonardville and Aranos to arrive at Union's End, South Africa. From Union's End the river bed, forming the Botswana border, meanders through the Kgalagadi Transfrontier Park for a distance of over 200 km. It reaches the southern boundary of the game reserve just north of Twee Rivieren Camp, near its confluence with the Auob River.
In the Kalahari, the Nossob is said to flow about once a century. However, water is stored underground to provide life for grass and camelthorn trees growing in the river bed. The Nossob may flow briefly after large thunderstorms, causing wildlife to flock to the river.