The basin consists largely of undulating terrain between ranges of hills and mountains. The northward flowing (South African) tributaries of the Limpopo river have incised deep gorges through the hills and mountain ranges that are visible as erosional remnants. Elsewhere, the river valleys are broad and flat-bottomed with river channels that are slightly or moderately incised into the surrounding parent material.

The upstream portion of the Limpopo is characteristically flat with kopjes and small hills rising not more than 200 m above the general level and occasional elongated ridges of more resistant strata forming the only local relief. The relief is more pronounced in the south-eastern corner where the quartzites of the Transvaal Sequence, which form the ridges of the Magaliesberg and the Witwatersrand, have been deeply incised by the river to depths of up to 600m. The Waterberg Plateau forms another area of more pronounced relief on the eastern side of the central portion of the basin.

Large portions of the central and western parts of the Limpopo basin (especially in the Shingwedzi and Letaba sub-catchments) have very little or poor drainage, and are usually considered to be endorheic (internally draining). These areas are often marked by the formation of saltpans or clay-bottomed pans where rainfall collects and evaporates. These areas are generally subjected to mechanical (physical) weathering processes, in contrast to the predominance of chemical weathering processes in the wetter headwater regions of most tributaries.

The Mozambique portion of the Limpopo basin consists of gently undulating terrain with numerous small tributary streams and pools forming part of the Changane drainage system. This tributary rises close to the Zimbabwe- Mozambique border, meanders across the Mozambique coastal plain and joins the Limpopo river very close to its mouth on the coast near the town of Xai-Xai. A belt of heavy textured soils connecting the Limpopo and Incomati river systems suggests that the Limpopo previously also entered the Indian Ocean via Maputo Bay.

A continuous belt of coastal sands of varying width occurs adjacent to the coast. The eastern border of these coastal sands is characterised by a series of high dunes generally parallel to the coast which normally attain their highest elevations just inland of the high water mark. Behind these dunes occur depressed areas with barrier lakes and related dunes.