The St Lucia estuarine system is a significant system as it comprises of 50% of the total estuarine area of South Africa. Freshwater and marine environments are interconnected and thus include a wide range of habitats for marine species and freshwater species to be present.

The marine environment around St Lucia is influenced by the Agulhas Current, one of the major western boundary currents of the world, as well as freshwater input from various rivers and rainfall. Both the current and freshwater input play a major role in nutrient loading of the marine species and environment.

Animal diversity in the St Lucia estuarine system include species from Microalgae, Benthic invertebrates (crabs molluscs, worms, ect), Zooplankton to fish fauna.

The Coelacanth, known only from fossils and thought to be extinct for 70 million years, was rediscovered in 1938 and observed in 2000 when the fish was found inhabiting canyons of the coast of iSimangaliso Wetland Park.

Humpback whales and Southern Right whales pass along the KwaZulu-Natal coast annually on a migration route between their summer polar feeding grounds in the Antarctic to the tropical and sub-tropical coastal waters of Northern Mozambique and Madagascar where they breed in the winter. These whales are commonly seen in the area from June to November every year. Whale watching trips operate daily from St Lucia during this time.