The Pongola River rises at some 2 200 m above mean sea level near Wakkerstroom, Mpumalanga, and descends steeply through the major portion of its catchment to the west of the Lebombo mountains. The Pongola passes between the Lebombo and Ubombo ranges through a narrow gorge (known as Pongolapoort) and the lower reaches of the river lie on the Maputuland coastal plain east of the mountains in northern KwaZulu-Natal.

Here, the river has a slope of 1 in 3 000; the abrupt change in gradient stems the flow rate of the river on the plain, causing a deposition of part of the sediment load and the flooding of extensive areas adjacent to the river course. This broad alluvial plain, known as the Pongola floodplain, extends from the gorge to the confluence of the Pongola and the Usutu rivers, close to the border with Mozambique.