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In a southern African context, Begg (1984a, 1984b) was probably the first to document the similarities and differences between the ichthyofaunal composition and structure in a large number (62) of estuaries comprising several different types of systems. He found that open subtropical estuaries in KwaZulu‐Natal Province were dominated by a wide variety of MEO fishes while systems that were normally closed were dominated by estuarine and freshwater species. Similar patterns exist between permanently open and periodically open estuaries in Western Australia (Valesini et al. 2014).

The pioneering work of Begg (1984b) laid the foundation for more detailed and wide ranging studies. Very quickly, it was determined that the individual estuarine characteristics, especially estuary typology is a key factor in the structuring of fish assemblages (Blaber 1985). Because no two estuaries are identical in terms of either biotic or abiotic characteristics, it could be argued that the ichthyofaunas of each estuary would also differ. Whitfield (1999) postulated, however, that if the fishes in estuaries respond to the environment in a consistent manner, the assemblages occupying similar types of estuaries in a particular region would be expected to reflect this similarity. This would apply particularly at a functional level where the biogeographical distributions of individual fish species does not matter.

Figure 2.6 Summary of importance of EUFG guilds (MS = marine straggler, MEO = marine estuarine‐opportunist; MMD = marine estuarine‐dependent, EM = estuarine migrant, E = solely estuarine, CA = catadromous, FEO = freshwater estuarine‐opportunist; FS = freshwater straggler) in (a) small closed estuaries (b), moderate‐to‐large closed estuaries (c) and predominantly open estuaries in the cool‐temperate, warm‐temperate and subtropical zoogeographic regions of South Africa (after Harrison & Whitfield 2008). Thick horizontal lines denote separation between EUFG categories (i.e. marine, estuarine, diadromous and freshwater).

Early indications that the above patterns and assumptions may be valid was provided by Vorwerk et al. (2003) who demonstrated that the fish assemblages in smaller and larger temporarily open/closed estuaries in the Eastern Cape Province of South Africa grouped together (according to size) and were very different from fish assemblages in permanently open estuaries within the same region (Figure 2.8). Similarly, Harrison & Whitfield (2008) recorded that the fish assemblages in South Africa differed between estuarine types, particularly within the warm‐temperate and subtropical regions, and noted that the numerical contribution of marine species, such as MEOs, was higher in permanently open than predominantly closed estuaries. This is probably a reflection of a permanent connection with the sea, which allows unrestricted access to permanently open estuaries, a conclusion supported by the occurrence of marine stragglers within these systems. Freshwater and estuarine species were generally more abundant in temporarily open/closed estuaries than in permanently open systems, probably also reflecting the degree of isolation from the sea. Bennett (1989) recorded that, in estuaries in the cool‐temperate Western Cape Province, MEO species dominated the fish community in the permanently open Palmiet Estuary while resident estuarine species dominated that in the nearby normally closed Bot Estuary.

Table 2.1 Number of fish species from five ecological guilds (DA = diadromous, FW = freshwater, ES = estuarine, MEO = marine estuarine‐opportunist, MS = marine straggler) per selected estuarine system in each of three European regions (data from Pihl et al. 2002; Akin et al. 2005; Leitão et al. 2007).

Region/estuary	Number of species in each guild	Total number of species
DA	FW	ES	MEO	MS
Baltic region
NW Åland	3	17	16	5	3	44
Göta	4	3	15	14	17	53
Gullmarsfjord	4	1	13	13	19	50
Darss‐Zingster	6	20	10	5	3	44
Oderhaff/Stettin	9	29	8	3	1	50
Boreal/NW Atlantic region
Weser & Elbe	9	33	12	16	8	78
Westerschelde	7	13	12	16	8	56
Oosterschelde	9	1	16	23	25	74
Ems‐Dollard	7	3	13	21	9	53
Loch Etive	4	1	14	9	22	50
Forth	7	0	10	9	19	45
Humber	9	18	15	16	27	85
Thames	8	21	19	22	40	110
Mersey	6	13	12	19	19	69
Somme	4	0	7	11	6	28
Seine	11	9	15	20	24	79
Loire	10	8	4	18	6	46
Bay of Cádiz	1	0	12	22	18	53
Guadalquivir	7	2	9	10	4	32
Ria de Aviero	7	4	15	16	13	55
Óbidos	4	0	9	21	11	45
Mondego	3	8	7	2	11	31
Tagus	5	4	12	29	34	84
Mira	5	1	17	19	19	61
Mediterranean region
Messolonghi	1	3	10	10	38	62
Ebro	3	2	3	4	0	12
Koycegiz	1	3	1	12	25	42

Figure 2.7 Representation by three EUFG categories (freshwater, diadromous and estuarine) and two guilds (MS = marine straggler, MEO = marine estuarine‐opportunist) in the three major European geographical regions.

Figure 2.8 nMDS plot of the estuarine fish assemblage data from the Eastern Cape Province, South Africa (after Vorwerk et al. 2003). The circled groups indicate estuaries with significantly different communities representing permanently open and small and large temporarily open/closed systems. Each sample is represented by a three‐letter code; the first two letters are an estuary code (BI = Bira, EK = East Kleinemonde, GF = Great Fish, GQ = Gqutywa, KK = Keiskamma, KP = Klein Palmiet, MG = Mgwalana, MP = Mpekweni, MT = Mtati, NG = Ngculura) and the third letter is a season code (S = Summer, W = Winter).

Similarly, estuarine type is also known to influence the fish fauna of south‐western Australian estuaries (Potter & Hyndes 1999, Tweedley et al. 2016). To illustrate this, in detail, data on the density of fish species from the nearshore waters of 15 south‐western Australian estuaries (Tweedley et al. 2017) were used to construct a Bray‐Curtis resemblance matrix and subjected to nMDS ordination and ANOSIM tests. When based on presence/absence fourth‐root transformed abundances, faunal composition differed with estuary type, i.e. permanently open (PO), intermittently open (IO), seasonally open (SO) or normally closed (NC) (Global R = 0.882; P = 0.1% and Global R = 0.806; P = 0.1%, respectively). On the associated nMDS plots, the estuaries from each type form discrete groups and progress across the plot from left to right in order of the decrease in the duration of opening (Figure 2.9a, b).

Permanently open estuaries contained the largest numbers of species (typically >40), and this declined to ~30 and ~25 in IO and SO systems, respectively, and generally ≤7 in NC estuaries (Figure 2.9c, d). Although all estuaries contained a core suite of estuarine species (i.e. E, EF and EM), the number of marine species (MS and MEO) were far lower in IO and SO than PO estuaries and were almost absent in NC systems (Figure 2.9e, f). This reflects the reduced connectivity with the ocean and the lack of opportunity for marine species to recruit and the fact that NC estuaries can often become markedly hypersaline (Hoeksema et al. 2018). When based on abundance, marine species, typically the juveniles of MEO taxa, can make a relatively large contribution to fish fauna of some permanently open estuaries (e.g. up to 45% in the Peel‐Harvey), with stragglers, by definition, making a very minor contribution (average in PO systems of 1.4% all fish; Figure 2.9e–h). Thus, the vast majority, i.e. 54–99.99%, of the fish in each system belong to the estuarine category. The contribution of the component guilds differed, however, among estuary type, with the proportion of EM species being 33% in PO systems vs 11 in SO and only 2 and 0.8% in IO and NC estuaries, respectively. In contrast, EF species numerically dominated IO systems (average = 67%), as these systems tend to be oligohaline, and E species, some of which have remarkable tolerances to salinity, dominated NC estuaries (average = 83%).

When it comes to assessing the dominant drivers governing the composition of estuarine fish assemblages, it would appear that biogeographical factors are very important. In this regard, an overall analysis based on the composition of the estuarine ichthyofauna in South African estuaries by Harrison & Whitfield (2008) revealed a tendency for subtropical, warm‐temperate and cool‐temperate systems to group together, regardless of estuary type. These findings place a whole new perspective on the role of estuarine typology versus biogeography, one that continues to influence our understanding of the structuring and functioning of fish assemblages in estuaries.