The climate of the basin varies spatially from being arid in the west through semi-arid and temperate areas in central zones to semi-arid in the east, with a few sub-humid pockets in the centre.

Three wind systems have been identified as having a strong influence on the basin’s climate. These are the tropical cyclones from the Indian Ocean; the southeasterly wind systems that bring rainfalls from the Indian Ocean; and the Inter-Tropical Convergence Zone (ITCZ), which in some years moves sufficiently far southwards to influence rainfalls in the northern parts of the basin.

Air temperatures across the basin show a marked seasonal cycle, with highest temperatures recorded during the early summer months and lowest temperatures during the cool, dry winter months. Rainfall is also highly seasonal, falling predominantly as intense convective thunderstorms during the warmer summer months.

The severe droughts observed during the early 1990s and the recent exceptional floods in the Limpopo valley illustrate the extreme variability of rainfall and runoff in the basin. This variation has significant effects on aquifer recharge.