The delta is divided into four areas, which are very different concerning their ecology and flora. The so called Panhandle, the underflow of the Okavango River, aquiferous permanently, is overgrown with papyrus species (Cyperus papyrus). The swamp areas at the end of the Panhandle, flooded permanently, are the second zone. This area creates a mosaic of open water surfaces and swimming islands. The areas at the periphery of the delta, which fall temporarily dry - the so called seasonal swamps - are the third zone. The large islands (Chief Island, Chitabe Island) inside the delta and the tongues of sand, which reach the delta from the south, are the fourth zone. Approx. 1,300 different plants species are identified in the whole delta area.
The shore vegetation is also very different, there are mopane and baikea woodlands in the northern part. But also areas of savannah, which are important for the African large mammals, semi-desert regions, grasslands and fields are surrounding the delta.