in the Embley Estuary in Australia, they are often inhabited by species found in those same habitats in the sea (Blaber 2000). In addition, the occurrence of stenohaline marine species within estuaries is severely restricted by the fluctuating salinities that are usually found in these systems (Harrison 2004, Aguilar‐Medrano et al. 2019).
A major factor that influences the occurrence and diversity of fishes in estuaries is zoogeography (Harrison & Whitfield 2008). In estuaries globally, fishes of marine origin tend to dominate the ichthyofauna, with more than half of both the number of species and number of individuals being either fully estuarine species (ES) or species of marine origin (MEO and MED) (Potter et al. 2015a). However, there will always be exceptions to the rule. Estuarine systems with a proportionally high river flow and oligohaline salinities often have a dominance of freshwater (FW) and/or diadromous (i.e. catadromous, CA and anadromous, AN), as well as amphidromous species, e.g. some tropical and subtropical estuaries in South America (Garcia et al. 2003, de Moura et al. 2012) or temperate estuaries in New Zealand (McDowall 1976, Jellyman et al. 1997).
The balance between the guilds has also been shown to change with increasing river flow, e.g. the proportion of marine species in the Great Fish Estuary (South Africa) declined, and that of freshwater and catadromous species rose with increasing river flow (Ter Morshuizen et al. 1996). Changes in fish assemblage composition are also evident during periods of drought (Martinho et al. 2007, 2010) and the increasing prevalence of climate change scenarios (Hallett et al. 2018). Similarly, physical alterations in the ecohydrology of estuaries can alter the guild composition of fish species within such systems, e.g. the addition of a second entrance channel in the Peel‐Harvey Estuary (Australia) increased marine connectivity and salinities, with a concomitant increase in marine taxa within this system (Potter et al. 2016). Fortunately, the advent of ecoengineering has meant that previously degraded estuaries can be partially or completely restored in terms of ecohydrology and therefore provide suitable habitat for more diverse and abundant fish guilds (Elliott et al. 2016).
In terms of the dominant taxa in tropical and subtropical estuaries throughout the world there are broad similarities, but also some interesting contrasts. On the African continent, similar families are recorded in both East and West African estuaries, but the species present are very different. Whitfield (2005) attributed the above pattern to free mixing of tropical fish species across the warm northern and southern extremities of the continent during the late Mesozoic and early Cenozoic, a process that ceased with the closure of the Tethyan Gateway in the north and the development of the cold Benguela upwelling system in the south. This allowed the ‘geminate’ species on the eastern and western coasts of Africa to develop into the current taxa present in the estuarine fish assemblages of these two regions.
In East Africa, there are limited ‘estuarine’ coastal waters and, although sciaenids are present, they are not a dominant component of the fauna as is the case in tropical and subtropical estuaries in other parts of the world where riverine influences on the marine environment are greater. Apart from sciaenids, other dominant families such as the engraulids, carangids, clupeids and haemulids are broadly comparable across all the above regions (Barletta & Blaber 2007). However, within the Indo‐West Pacific, clupeids and engraulids are far more diverse and numerous in the estuarine coastal waters of equatorial south‐east Asia than in other areas (Blaber 2000).
There are important differences in the relative proportions of tropical freshwater species, both between and within regions. Freshwater species make up more of the fish fauna in tropical Atlantic estuaries (Barletta et al. 2005) than in the Indo‐West Pacific or East Pacific, particularly in South America, where many of the very diverse fauna of siluriid catfishes are common in estuaries that are dominated by freshwater inputs and oligohaline conditions are widespread. Similarly, in West Africa various silurids and cichlids make a significant contribution to estuarine communities that receive strong riverine inflows. Localised differences in estuarine fish assemblage composition may be related to differences in the amount of catchment rainfall, with run‐off in some systems so great that it leads to a degree of ‘estuarisation’ of adjacent coastal waters (Able 2005, Whitfield 2005, Jaureguizar et al. 2006).
In more arid parts of the world (e.g. much of Australia and South Africa), freshwater fish species are usually not significant components of the estuarine fish fauna where polyhaline and euhaline salinities are prevalent (e.g. Blaber et al. 1989, Valesini et al. 2014, Whitfield 2015). The estuaries in equatorial regions of south‐east Asia have rather more freshwater species than other areas of the Indo‐West Pacific but, despite the high diversity of freshwater fish faunas in Borneo and Sumatra (Hubert et al. 2015), relatively few fish species live in estuaries. Higher rainfall areas, e.g. eastern South America, western Africa, south‐east Asia, which are classified as tropical rainforest or monsoonal climates (Kottek et al. 2006), may provide a greater input of fresh water into estuaries and a high representation of freshwater fish taxa. In comparison, lower rainfall areas of eastern and southern Africa and Australia result in polyhaline or euhaline estuarine waters that are dominated by marine and estuarine fish species (Potter et al. 1990).
Moreover, in the case of the Indo‐west Pacific, freshwater systems on the Sunda Shelf (e.g. Java, Borneo and Sumatra) contain predominantly primary freshwater fish (sensu Myers 1949) and thus these species have no tolerance to saline water (Hubert et al. 2015). In contrast, areas to the south east of Wallace's line (e.g. Wallacea, New Guinea and northern Australia) are dominated by peripheral division fish, including amphidromous species, which have a marine origin and thus could colonise estuaries (Unmack 2001, Tweedley et al. 2013). Nevertheless, with regard to the proportions of freshwater species, it is probable that other factors, such as the greater diversity of possibly preadapted Siluriiformes, are important (Blaber 2000). Perhaps one of the best examples of changing fish assemblages between river catchment and coast is from the Caribbean (Central America) study by Winemiller & Leslie (1992) who found that different suites of common fish species characterized streams, rivers, estuarine lagoons and sea.
Salinity regimes are a major driver in determining which fish species/groups dominate particular estuaries, with those taxa with the strongest euryhaline characteristics being best adapted to colonise most types of estuaries, ranging from predominantly oligohaline to hyperhaline. Indeed, the ability of a fish to utilise a particular habitat within an estuary is primarily dependent on that species being able to tolerate the salinity regime associated with that habitat (Whitfield et al. 2006, Smyth & Elliott 2016). The most successful and widespread estuary‐associated species globally are those that are highly euryhaline such as the oxeye tarpon Megalops cyprinoides and flathead mullet Mugil cephalus (Krispyn et al. 2021). Of the four major ichthyological categories present in South African estuaries, elasmobranchs are most prevalent under euhaline conditions, marine fish species under euhaline, polyhaline and mesohaline conditions, estuarine‐resident species under polyhaline, mesohaline and oligohaline conditions, and freshwater fish species under oligohaline conditions (Whitfield 2019). Overall, the fish species best adapted to hyperhaline conditions were marine teleosts but these conditions occurred in only a few estuaries on the subcontinent.
Based on multivariate analyses of South African ichthyofaunas, Harrison (2002) identified three biogeographic provinces, i.e. a subtropical east coast, a warm‐temperate south coast and a cool‐temperate west coast (Figure 2.1). As one moves from the subtropical east coast around towards the cool‐temperate west coast, estuarine fish diversity declines (Wallace & van der Elst 1975). This is linked to the attenuation in the distribution of tropical species, with the fauna of east coast estuaries dominated by subtropical and tropical Indo‐Pacific species (Blaber 1981). Towards the warm‐temperate south coast, there is a marked change and the percentage contribution of tropical species decreases while that of temperate species increases. The fish faunas of the estuaries on the cool‐temperate west coast have a much lower diversity and comprise mostly cosmopolitan species or cool water endemic taxa (Harrison 2005). In a subsequent more detailed analysis, using presence/absence, abundance and biomass data, Harrison & Whitfield (2008) showed that the fish assemblages in the different biogeographic regions were
