The Park, lying on the interface between tropical and sub-tropical biota with varied geomorphic and climatic conditions, supports an exceptional ecological and biological diversity, especially of wetlands.
The distribution of the vegetation is largely determined by topography, moisture regimes and edaphic conditions. The system is almost pristine and still functions well. It is a rich mosaic of savanna grassland, thickets and woodlands; grasslands: low-lying, hygrophilous and floodplain; sedge swamps, freshwater reed and papyrus swamps; riverine woodlands, swamp forests and forested dunes; the lake with its uniquely variable salinity regime; underwater macrophyte beds, saline reed swamps, saltmarshes and mangroves; sandy and rocky shores, coral reefs and submarine canyons.
The Park is at the southernmost end of the Maputaland Centre of Endemism (van Wyk, 1993) which extends from the Limpopo to the St Lucia estuaries, east of the Lubombo mountains. It is one of two foci of high endemism in the Tongaland-Pondoland Regional Mosaic described by White (1983). The flora is diverse, having 152 families, 734 genera and 2,173 species. 98% of Maputaland Centre species, approximately 9% of the flora of South Africa and 31% of the flora of KwaZulu-Natal, have been recorded in the Park (Scott-Shaw, 1994). 32 species are listed in the South Africa Red Data Book for Plants and 8 species are contained in CITES appendices. 6 species are endemic to KwaZulu-Natal and 3 species are known only from the Park.
In the Maputaland Centre at least 168 species and subspecies are considered endemic or near-endemic (van Wyk,1993). Of these, 44 (27%) are found in the Park. The following species are of phytogeographic interest: Helichrysopsis septentrionale (Maputaland endemic), four regional endemic genera (Brachychloa, Ephippiocarpa, Helichrysopsis and Inhambanella), Restio zuluensis, an endemic, Wolffiella welwitschii, a recently discovered endemic, the smallest flowering plant in southern Africa and Thalassodendron ciliatum, the only marine flowering plant found on the south African coastline. A new small grassland aloe with affinities to Aloe parviflora awaits description. It is endemic to the Park and confined to the Eastern Shores area. Kalanchoe luciae lucia, described recently, and Rhus kwazuluana, are also endemic to the Park. 136 species are at their southern limit and there are some notable disjunct distributions.
The Mkusi River swamps are diverse and undisturbed with a forest of Ficus, Voacanga, Ilex, Uera and Syzygium species. The wetlands of the estuarine system include freshwater Phragmites australis – Cyperus papyrus swamp which covers approximately 7,000 ha in the Park, forming the largest protected wetland in South Africa; saline reed swamp on alluvium and islands in Lake St Lucia, dominated by Phragmites mauritianus; sedge swamp, mainly in the Mfabeni swamp, characterised by Eleocharis limosa; salt marsh dominated by Sporobolus virginicus and Paspalum vaginatum with Juncus kraussii (ncema, commercially used by local people), and nutrient-rich submerged macrophyte beds on saline lake-bed soils.
Aquatic vegetation such as the pondweed Potamogiton pectinatus develops in the lake after it has been low for a long period, which supports much birdlife. Grassland types include hydrophilous grassland on sandy riverine soils dominated by Acroceras macrum and Ischaemum arcuatum; high-lying grasslands on sand – a fire-subclimax community, palm-veld with Hyphaene coriacea and Phoenix reclinata, also a fire-subclimax community; Echinochloa floodplain grassland; and low-lying grasslands on clay.
Open woodlands include mixed Acacia/broad-leaved woodland of Hyphaene coriacea and Ziziphus mucronata and mixed Acacia woodland of Acacia nigrescens, A.gerrardii, A.tortilis, A.nilotica, which provide grazing and browsing for herbivores.
Closed woodlands are found on low-lying drainage lines and older alluvial soils, especially along the Mkuze and Msunduzi rivers. They include riverine Ficus sycomorus and Acacia xanthophloea; mixed Acacia closed woodland of A.tortilis and A.nilotica; broad-leaved woodland of Combretum molle and Zizphus mucronata, and Terminalia sericea-Strychnos woodland and scrub.
Thickets of mixed microphyllous and broad-leaved woodland subject to salt spray and wind occur on seaward-facing dune slopes with Eugenia, Brachylaena, Euclea, Diosporos and Mimusops species.
Forest types include swamp forest, rare in South Africa, covering 3,095ha (64% of the South African total) dominated by Ficus tricopoda, hygrophilous forest and Barringtonia racemosa forest. These occur on organic soils in hypo-saline drainage lines and marshes around freshwater lakes usually flooded with slow-flowing water after rains; mangroves, dominated by Bruguieria gymnorrhiza and Avicennia marina; the uniquely well developed coastal dune forest of Mimusops caffra, Grewia occidentalis and Psychotria capensis which can reach 30m high and has a dense shrub layer with many lianas; sand forest on relict dunes of highly-leached sands with Newtonia hildebrandtii and Cleistanthus schlechteri; and coastal lowland forest growing to 30m high on highly leached sands with Strychnos decussata and S. gerrardii with species of Terminalia, Balanaites and Sclerocarpia, also plantations of Pinus elliottii.
In the marine flora, 325 seaweeds have been recorded in the Park, nearly 78% of the total seaweeds of the Kwazulu-Natal coastline. A new species, Cellophycus condominius, and a parasitic red alga, Calocopsis smithenae, have recently been found; also beds of kelp Ecklonia biruncinata, deep in submarine canyons.