The Nambung River was encountered by explorer George Grey on 16 April 1839, during his second disastrous expedition along the Western Australian coast.

[3] The river was recorded as the Namban in 1875 by Staff-Commander William Edwin Archdeacon R.N., who was in charge of the Admiralty survey of the coast of Western Australia.

The river terminates at the surface in limestone karst terrain 9 km south-south-east of Cervantes, 5.5 kilometres (3 mi) from the Indian Ocean coast.

Large areas of Swan Coastal Plain native bush land are well preserved within the lower reaches of the Nambung river system, dominantly comprising low scrub heath (less than 2 metres (7 ft) tall).

Most lagoons and lakelets in the area are isolated from the sea and from surface creek drainage, being fed by rainfall and groundwater flow from surrounding dunes and limestone.

There is a complicated hydrology with examples of 1 kilometre (1 mi) long lakes appearing virtually overnight and solution pipes spouting columns of water.

Much of this discharge flows through karstic solution channels in the Tamala limestone, a calcareous and siliceous formation deposited in the middle to late Pleistocene (1,500,000-10,000 years ago).