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Estuaries are transitional water bodies that represent the meeting place between rivers or land‐based freshwater run‐off and the sea. Within this system and its associated catchment and marine areas, there is a set of ecotones, i.e. gradations between the different systems (Basset et al. 2013). These ecotones cover the freshwater‐estuary, estuary‐marine, surface‐water column‐bed (vertical) and estuary to the sides (lateral) of systems. Each of these ecotones cover a gradation or even an abrupt change in environmental characteristics. This in turn creates ecoclines, the gradients of change on the biotic and environmental variables. The horizontal ecocline between the freshwater and marine fish components associated with estuaries is often steep (Whitfield et al. 2012). In contrast, the ecocline in fish assemblages between the estuary and the marine environment is usually more gradual (Chaves et al. 2018) and may even extend a considerable distance into the sea (McHugh 1967, Araújo et al. 2002). In some cases, these two different ecoclines may overlap within a single region of an estuary, e.g. in the Thames system there were overlapping gradients for freshwater species from the river to the mid‐estuary region, and for marine species, the gradient was from the sea to the mid‐estuary (Attrill & Rundle 2002).

Although the environmental (physico‐chemical) transition from the sea through the estuary and into the river catchment or watershed may appear gradual (Table 1.1, Basset et al. 2013), the changes between these different aquatic environments represent, for many fish species, major potential barriers (Blaber 1991, Martino & Able 2003), which can be likened to the obstacles facing labyrinthodonts making the transition from water to land! Thus, the assumption that most freshwater and marine fish species have relatively free access to the abundant and diverse food resources and habitats provided by estuaries is a fallacy that is not supported by ichthyological studies that traverse these ecosystem boundaries or transition zones (Barletta et al. 2008).

All fish species have a set of well‐defined tolerances to environmental characteristics, and those tolerances may remain constant or change during their lifecycles, for example the ability by some taxa to live for part of their lives in the sea, estuary or catchment. Most fish species, especially those which have life cycles closely tied to either rivers or the sea, are generally confined to those particular aquatic environments and seldom stray into estuaries (Whitfield et al. 2017). However, those taxa that are able, because of their tolerances, to traverse the ecological divisions have access to highly productive waters that provide ideal nurseries and adult feeding grounds for a variety of fish trophic groups (Elliott & Hemingway 2008).

Table 1.1 Geographic divisions, salinity ranges and zones (Venice System) and the approximate distribution of different categories of ichthyofauna found in a ‘generalized’ estuary

(modified from an estuarine invertebrate concept published by Carriker 1967).

Estuary divisions	Salinity ranges	Salinity zones	Fishes and approximate distribution range within estuaries
River reaches	<0.5	Limnetic	Anadromous migrants	Freshwater taxa Stenohalinemarine taxa	Estuarine residents	Euryhaline marine taxa	Catadromous migrants
Estuary head	0.5–5	Oligohaline
Upper reaches	5–18	Mesohaline
Middle reaches	18–25	Polyhaline
Lower reaches	25–30	Polyhaline
Estuary mouth	30–40	Euhaline

There is little doubt that the highly variable and sometimes widely fluctuating physico‐chemical conditions in estuaries are a challenge to many marine or freshwater fish species that would otherwise make extensive use of these systems (Haedrich 1983, Cowan et al. 2013). However, those taxa that are euryoecious (i.e. a wide ability for various variables, including euryhaline for salinity and eurythermal for temperature) and eurytopic have been able to exploit estuaries and have the benefit of occupying one of the most productive natural aquatic ecosystems on the planet (Day et al. 2013). This gave rise to the idea of the stress‐subsidy phenomenon in which a highly variable environment is stressful for those species not able to tolerate the conditions but a subsidy for those able to tolerate the varying conditions, and thus thrive (Elliott & Quintino 2019).

Some marine species have become so closely associated with estuarine systems that they are termed ‘estuary dependent’, especially in terms of nursery area use by the juveniles (Miller et al. 1984). This term has been widely and often loosely used to refer to a wide range of fish species that are found in estuaries (Able 2005). In reality, there is a cline in the association by fish taxa found in estuaries (Figure 1.1), ranging from those species that are completely dependent on estuaries for at least part or all of their life cycle, to those fish that are most abundant in either marine or freshwater environments and only use estuaries opportunistically to varying degrees (Elliott et al. 2007, Potter et al. 2015, Whitfield 2020).

The occupation of an estuary by a particular fish species depends on the availability of a suitable niche for that species. As an initial model, Figure 1.2 summarises the way in which a niche is produced and then occupied by fishes within estuaries, but it also illustrates that most of the driving variables are prone to anthropogenic impacts from a variety of sources. The nature and extent of these impacts feature in a number of chapters within this book (see Chapters 6–11 in particular) and highlight the major role that humans play in determining the future of estuarine fish assemblages going forward. In reality, the full range of abiotic and biotic drivers of fish assemblage structure is very complex and diverse, with a simplified depiction of known factors influencing southern African fish communities being shown in Figure 1.3. Despite having worked on some of these drivers for several decades, it would be true to say that, in many instances, our current understanding of the detailed influences on estuarine fish communities is still in its infancy.

Figure 1.1 Diagrammatic representation of the gradual change in the level of estuary association by fish guilds not dependent on estuaries (lower left) to those completely dependent on estuaries (upper right) (after Whitfield 2020).