The fauna and flora of estuaries are typically capable of tolerating the above- mentioned changes. A comparison of an estuarine flora and fauna with that of a neighboring marine reef will show that there are many species, both plant and animal, which are either excluded by these changing conditions or avoid estuaries. Those that can tolerate the estuarine environment are often very successful and abundant in their chosen environment, e.g. sand prawns Callianassa kraussi and mudprawns Upogebia africana, mullet and fish that feed on the bottom or eat plankton.
A feature of the life styles of a variety of estuarine species is migration. Most of the larger fish species as well as invertebrates such as the estuarine swimming prawns and the mangrove crab Scylla serrata breed at sea where salinity, temperature and oxygen availability are much more constant than in an estuary. This favours the sensitive larval stages which then, at a later stage of development, move to the estuarine nursery grounds for a time to grow and develop into mature animals before migrating back to the sea. In invertebrates such as the swimming prawns or fish like the Cape stumpnose Rhabdosargus holubi there is no return migration. Fish like grunter Pomadasys commersonnii may move repeatedly between marine spawning grounds and estuarine nursery or feeding grounds as at St Lucia. It is incorrect therefore to describe estuaries as breeding grounds, except in the case of resident species and even here it has been shown that apparent residents such as the mud prawn synchronise egg hatching to coincide with ebb tides such that newly hatched larvae are transported out to sea where they develop for a time before returning to the estuary (Wooldridge, 1994). From the above, it is clear that the time of the year that the mouth is closed or open is very important and can have a major effect on the nature of estuarine fauna."
If one considers the major habitats in estuaries it is clear that the different plant types often play a major role. Within the water column the phytoplankton, and microscopic single-celled plants (diatoms), provide a source of food for filter-feeders. The fixed, much larger plant species are extremely significant, whether in the form of the generally submerged seagrasses, intertidal saltmarshes of temperate regions or the mangroves of more tropical areas. The development of the seagrasses and to some extent the saltmarshes is greater in areas of clearer rather than turbid water which limits light penetration. Clearly mangroves are not affected by water turbidity except possibly in the very early stages of establishment of propagules (seedlings). Seagrasses can survive in non-tidal conditions where their distribution may be limited by salinity, as in the St Lucia system, but mangroves and salt marshes require a tidal regime for survival. The roots of mangroves cannot tolerate long term immersion in the waterlogged, low sediments where they are rooted. These macrophytes all contribute to the formation of a three dimensional environment and thereby provide major habitat types for sheltering small fish and invertebrates.
Estuaries depend on a basic input of carbon as a food supply. This may arise from a variety of sources, e.g. local plant growth in the shape of mangroves, reeds, saltmarsh vegetation, phytoplankton or microscopic one celled plants called diatoms which are found on intertidal mudflats. They also depend upon the input of leaves and other plant litter brought in from the catchment or even marine seaweeds washed in by tidal currents. Little of the macrophytic material mentioned above appears to be consumed in the fresh form. Instead, it contributes to the detrital food chain whereby it is colonized by bacteria and fungi which convert the often indigestible carbon material into more easily assimilable carbohydrates and proteins.
Tidal currents play a vital role in dispersing this material throughout the estuary thereby making it available to filter feeders. These organisms are represented by animals such as mudprawns, various mussel species and surface deposit feeders such as crabs which forage during low tide on the material deposited during the preceding high tide, or slack water period.
Fine detrital material in sediments is also used by many of the estuarine mullet species which, are often a very abundant component of estuarine fish communities. These are in turn preyed on by large fish eating birds such as cormorants, herons, fish eagles and crocodiles in systems like St. Lucia.