The Limpopo river has a relatively dense network of more than 20 tributary streams and rivers, though most of these tributaries have either seasonal or episodic flows. In historical times, the Limpopo river was a strong-flowing perennial river but is now regarded as a weak perennial river where flows frequently cease. During drought periods, no surface water is present over large stretches of the middle and lower reaches of the river.

The Crocodile river is the largest of the Limpopo tributaries in terms of both its catchment area and volume of flow, draining an area of 29,600 sq km. The Crocodile joins the Marico river some 250 km from its source to form the main stem of the Limpopo river. However, the Hartbeespoort dam commands a large portion of the total catchment runoff for the Crocodile river.

The Notwane river is another major and important tributary of the Limpopo river. It rises on the edge of the Kalahari in Botswana, flowing in a north-easterly direction until it reaches the Limpopo river about 50 km downstream of the confluence of the Crocodile and Marico rivers. The Notwane river has a catchment area of 18,053 sq km.

The other tributaries of the Limpopo river are the Bonwapitse and Mahalapswe rivers, which rise in Botswana and flow in a mainly easterly direction to the Limpopo river, draining a combined catchment area of 42,090 sq km. The contribution to flow in the Limpopo river from these two rivers is appreciably lower than the tributaries draining from South Africa. There is normally no surface runoff during the winter months in these rivers.

The Matlabas, Mokolo and Lephalala rivers are three of the main right-bank tributaries in a downstream sequence, joining the Limpopo river upstream of the Sterkloop/Seleka Farm flow gauge. These rivers flow in a mainly northerly direction, draining a combined area of about 36,180 sq km. The flow pattern in these tributaries is very irregular as a result of low rainfall and appreciable transmission losses. Normally there are long periods of no flow during winter months.

Other major sub-catchments of the Limpopo include the Shashe river, which rises in Botswana and has the Ramokgwebana, Simukwe, Shashani and Tuli rivers as its tributaries. The Umzingwani river is another major tributary of the Limpopo, draining a catchment area of about 12,600 sq km.

Other sub-catchments of the Limpopo river include the Lotsane, Motloutse, Bubi, Nzhelele, Sand, Mwenezi, Olifants, Luvuvhu, Shingwedzi, Letaba, Changane and Mogalakwena river catchments.