recruitment of estuarine fishes. Such degradation is evident in Europe (Rochette et al. 2010, Franca et al. 2012) and North America (Ruiz et al. 1993, Morley et al. 2012). A counterintuitive example for the San Francisco Bay and Delta documents the increase in littoral fishes, primarily associated with nearshore juvenile nurseries that are increasingly dominated by invasive aquatic plants (Mahardja et al. 2017), a contrast to the concomitant declines in reproductive success of pelagic fishes in this system (Sommers et al. 2007).
Plant invasions of estuaries are common and can degrade habitat, but few are known to affect fish populations in temperate estuaries. One exception is the invasion of Phragmites australis into salt marshes across the northeastern USA in the last 100 years (Chambers et al. 1999) during which a European lineage of P. australis has aggressively displaced native marsh grasses (Saltonstall 2002, Myerson et al. 2010). The result is that marsh surfaces have been elevated, with losses of surface standing water that serve as nursery habitat for resident fishes such as Fundulus heteroclitus (Windham & Lathrop 1999, Lathrop et al. 2003, Osgood et al. 2003). The marsh alterations become more pronounced as the P. australis invasion progresses (Able et al. 2003, Lathrop et al. 2003, Hunter et al. 2006).
Urbanisation of estuaries is increasingly common and often occurs along altered shorelines, resulting in losses of shallow‐water refuge (Furukawa & Okada 2006, Wolanski et al. 2019 and references therein). Degradations of estuaries that could result in reduced reproductive and recruitment success are observed in numerous estuaries, for example the James River sub‐estuary in Chesapeake Bay (Bilkovic & Roggero 2008), estuaries in New England (Bertness et al. 2002, Able & Grothues 2018) and other temperate (Balouskus & Targett 2018, Crum et al. 2018) and subtropical (Krebs et al. 2014) regions.
Many estuaries are artificially channelled or canalised in the lower reaches, resulting in a loss of shallow water refuge for young fishes (Macura et al. 2016). A case from the Kowie Estuary in South Africa demonstrated the lower abundance of early developmental stages in canalised marina areas when compared to natural estuary margins – canalisation reduces vegetation cover and shallow refuge increasing the level of predation on young fishes in these areas (Kruger & Strydom 2010).
In a clear example of urbanisation effects on young‐of‐the‐year fishes, habitat‐specific research in the heavily impacted Hudson Estuary (USA) demonstrated the negative effects of shading by large piers on growth and abundance of the age 0+ pleuronectid Pseudopleuronectes americanus and labrid Tautoga onitis (Able et al. 1998, 1999, Duffy‐Anderson & Able 1999, 2001, Metzger et al. 2001, Duffy‐Anderson et al. 2003, Able & Duffy‐Anderson 2006, Grothues & Able 2020). Similar negative effects of shading by large over‐water human‐built structures were reported for migrating salmonids in the Pacific Northwest of North America (Ono & Simenstad 2014).
3.5.3 Impoundments and flow regulation
Impoundments, dams and alterations in freshwater flow are clear impediments to estuarine connectivity and function and often their support of fish reproduction (Livingston et al. 1997, Grange et al. 2000, Niklitschek & Secor 2005, Ritter et al. 2008, Kettle et al. 2011, Schreier & Stevens 2020). Impoundments on rivers and freshwater abstraction can profoundly affect the physical and chemical aspects of watersheds (Pringle, 2000), particularly downstream estuaries. A perusal of published literature indicates that freshwater abstraction can lead to shifts in trophic structure in estuaries, including that for fish assemblages and their distribution (Ter Morshuizen et al. 1996, Livingston et al. 1997, Tsou & Matheson 2002, Rubec et al. 2006, Sheaves & Johnston 2008) and reductions in year‐class strength (Strydom et al. 2002, Staunton‐Smith et al. 2004, Halliday et al. 2008). Impoundments and dams on estuarine tributaries clearly limit access to spawning areas for anadromous species (e.g. Beasley & Hightower 2000, Freeman et al. 2003, Walter & Merritts 2008, Limburg & Waldman 2009, Mattocks et al. 2017). Effects have been especially problematic for many salmonids and acipenserids (Levings 2016, Quinn 2018, Faulkner et al. 2019, Zarri et al. 2019).
Reductions in freshwater discharge and flows to estuaries through removals of water for agriculture and urban use may have profound effects on reproductive and recruitment potentials (Freeman et al. 2003, Limburg & Waldman 2009, Strydom 2015, Mattocks et al. 2017). Dredging to maintain channels and diversions of freshwater modify flows, alter hydrodynamics and degrade spawning habitats. Amongst the best examples are those for the Sacramento–San Joaquin Delta and estuary system in California in which the salmonid Oncorhynchus tshawytscha, the osmerid Hypomesus transpacificus and other, primarily pelagic, estuary‐dependent species have experienced failed recruitment and declined dramatically in response to critically low freshwater discharges (Kimmerer 2002, Sommers et al. 2007, Moyle et al. 2016). Managing freshwater flows in impounded estuarine systems may improve retention of eggs and larvae and improve recruitment potential, as reported for the engraulid Engraulis encrasicolus in the Guadiana Estuary, Portugal (Morais et al. 2012). Alternatively, anthropogenically altered and excessive freshwater flow from interbasin water transfers can adversely affect nursery function (Strydom et al. 2002).
3.5.4 Power plants
Power plants for electricity generation frequently have been built on estuaries or their tributaries (e.g. Kennish & Lutz 1984, Cattrijsse et al. 2002) and may threaten production and recruitment of estuarine fishes (McLusky & Elliott 2004), including anadromous salmonids and alosines (Taverny 1990, Costa et al. 2002). For decades it has been recognised that these plants present multiple threats to reproduction and recruitment of resident and anadromous fishes through (i) habitat destruction/modification during power plant construction; (ii) releases of effluent cooling water with temperatures far above ambient that may exceed tolerances of fish eggs and larvae; (iii) entrainment and impingement of early‐life stages in waters drawn from the estuary to cool condensers; (iv) discharge of chlorinated by‐products where antifouling methods are used and (v) effects on behaviour of spawning adults and recruiting juveniles. Precautions and regulations usually limit the extent of damage from power plant operations (Barnthouse 2013), but they are, in some instances, a substantial source of mortality to young fishes (NRDC 2014), for example through impingement of dominant species, including the osmerid Osmerus eperlanus and clupeids Clupea harengus and Sprattus sprattus (Greenwood 2008).
3.5.5 Estuary contaminants: water quality degradation
Contaminants and toxins are frequent components of estuarine waters, especially where the surrounding watershed is extensively developed or industrialised (Lawrence & Hemingway 2003, Day et al. 2013, Weis 2014). Still, we often have poor understanding of contaminant effects on estuarine fish reproduction and recruitment. Potential contaminants are diverse and can include those known for decades, e.g. metals, petroleum hydrocarbons, pesticides, industrial chemicals, nutrients and sewage (Weis 2014). Other contaminants are only recently recognised, for example endocrine disruptors that can influence sex determination (Rochman et al. 2014) and microplastics (Oliveira et al. 2013, Rochman et al. 2013, Critchell et al. 2019) that may impact reproduction or recruitment. Research currently underway in South African surf zones shows extensive consumption of microplastics by an estuary‐associated mugilid Chelon richardsonii. Its larval stage feeding in surf zones is at risk for high consumption of microplastics entrained in rip channels (McGregor & Strydom 2020).
One exception to our limited knowledge of contaminant effects on estuarine‐occurring fishes is that for the fundulid Fundulus heteroclitus, which has been well studied in laboratory research. Exposure to mercury causes reduced fertilisation success (Khan & Weis 1987a, 1987b), embryonic deformities (Weis & Weis 1977a, 1977b) and reduced larval swimming and feeding ability (Zhou et al. 2001). Mercury also causes reduced predator avoidance by the larvae (Zhou & Weis 1998) and diminished prey capture ability by juveniles (Smith & Weis 1997). The accumulated evidence indicates that contaminated nursery sites contribute to reduced recruitment of this common species because of higher mortality in early‐life stages, slower growth and reduced condition and longevity (Weis et al. 2001). In an urbanised estuarine nursery area in South Africa,