The dominant soil types of the basin are moderately deep sandy to sandy-clay loams in the south, grading to shallower sandy soils in the north and deeper sandy soils in the west and east. The deeper loam soils are extremely important for agricultural activities and support extensive irrigation developments along many of the tributary rivers in South Africa, such as the Crocodile river catchment. A few extensive areas of black vertisols in the southern parts of the basin also support important agricultural developments.

Deep layers of wind-blown Kalahari sands cover large areas of the western portion of the Limpopo basin, while the sandy soils of the eastern (Mozambique) portion are derived from old, unconsolidated marine sands. These sandy soils support important hardwood timber resources.

The valley bottom soils along all of the tributary rivers and the Limpopo main channels are generally of colluvial or alluvial origin and support extensive areas of commercial and subsistence agriculture. In contrast, hilly or steeply sloping areas have fragile, shallow, stony soils with little agricultural potential. In the endorheic areas, most soils have a relatively high sodium and clay content.