The main arm of the Hunter River starts north of Muswellbrook and flows south where it is joined by the Goulburn River, and then east to Newcastle (map). It covers a distance of 467 km, and on average will discharge 1 800 000 megalitres of water to the sea per annum. Most of the water in the Hunter catchment comes from the north-eastern part of the catchment. The major tributaries of the Hunter River include:

1. Pages and Isis rivers, and Middle and Dart brooks rise in the Liverpool Ranges, with Stewarts, Moonan, and Omadale brooks, rising in the Barrington Tops (> 1570m above sea level).
2. The Goulburn River drains almost half of the catchment but contributes only 23% of the river flow.
3. The Paterson and Williams rivers drain the wetter area to the north-east of the catchment, arising in the Barrington Tops (> 1400m asl).
4. Wollombi Brook, draining the south-eastern segment of the catchment and rising in the Hunter Range (c. 440m asl).

The Hunter River upstream of the Hunter–Goulburn confluence has both regulated and unregulated sections. The main stem of the river is regulated by the Glenbawn Dam that helps to control flooding and provides a secure source of water for industry, town and irrigation use. Glenbawn Dam stores 750 000 megalitres and has a flood mitigation capacity of 120 000 megalitres. Water captured in the flood mitigation zone of the dam during floods is released when downstream flooding subsides, reducing the occurrence of peak flood flows and extending periods of moderately high flows after a flood event.