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The numerous habitat types have resulted in high species diversity.

There are at least 24 Acacia species and 8 Commiphora species, amongst other. Other vegetation of the area is a typically short fairly dense growth of shrubby Mopane trees, generally associated with a number of other trees and shrubs and a somewhat sparse and tufted grassveld. The riparian fringe of the Limpopo is of prime importance from the point of view of conservation. It is a dense vegetation community with a closed canopy which occurs in the rich alluvial deposits along the river.

The most striking trees in this community fever trees, Ana trees, Leadwoods, Fig trees and acacias. Extensive patches of this vegetation have been cleared for cultivation elsewhere along the length of the Limpopo River. The Limpopo floodplain has allowed some trees to grow to massive sizes. Nyala berries and Ana trees can get particularly big.

There are also some very large baobabs in the park, with one specimen having a circumference of 31m.