causes, but sub‐lethal impacts often are not appreciated (Rose 2000, O'Connell et al. 2004). Below, we briefly describe threats to reproduction and recruitment of estuary‐associated fishes. These threats are largely attributable to human activities (e.g. overfishing; habitat destruction; impoundments and freshwater‐flow regulation; power plants; deteriorating water quality with associated increases in contaminants; eutrophication; urbanisation; climate change and associated degradation and manmade and natural catastrophes). These occur disproportionately in estuaries and their catchments relative to other marine ecosystems, adding to concerns regarding threats to success of reproduction and recruitment in estuary‐associated fishes.
3.5.1 Excessive fishing: depletion of adults and by‐catch of juveniles
Heavy exploitation and excessive fishing, including by‐catch, have led to depletion of some estuary‐dependent and ‐associated fish stocks (Blaber et al. 2000). The cases for salmonids are well known (Levings 2016) in which overfishing is a major factor leading to declining recruitment. In a well‐documented case for a moronid, Morone saxatilis was overfished on the east coast of the USA, leading to failed recruitment and declared fishing moratoria (Richards & Rago 1999). Declines in alosine fishes in the northern hemisphere are in part due to overfishing, including unintended by‐catch, combined with habitat degradation (Limburg & Waldman 2009). These same factors are responsible for declines in recruitment of anguillids (Tesch 2003) and acipenserids (Van Winkle et al. 2002) in the Northern Hemisphere, as well as sciaenids (Cowley et al. 2008) and sparids (Bennett et al. 2017) in the Southern Hemisphere. Unintended by‐catch of adult and juvenile fishes is problematic in many fisheries (Davis 2002) and may be a threat to reproduction and recruitment success in estuary‐associated fishes. A notable example is that for by‐catch of juveniles of the sciaenid Micropogonias undulatus in shrimp trawl fisheries in which the large by‐catches may have different impacts on regional recruitment levels in the southeastern USA and Gulf of Mexico (Diamond et al. 1999, 2000).
3.5.2 Habitat destruction and degradation
Habitat destruction in estuaries began with human settlement and conversion of many marshes into agricultural lands or modified by dredging and filling (Gedan et al. 2009, Gedan and Silliman 2009). Another obvious and ongoing form of habitat destruction results from the cumulative effects of urbanisation (Wolanski et al. 2019).
In Chesapeake Bay, increasing sediment loads and higher turbidity have led to lower seagrass abundance and productivity (Kemp et al. 2005), reducing seagrass habitats that are important for juvenile fish production. Somewhat similarly, deforestation in the Columbia River watershed has increased sedimentation and decreased stream shading and thus negatively affects Pacific salmon habitats that serve as spawning areas and nurseries (Kelly et al. 1999). One subtle but frequent form of habitat degradation in estuaries is the elimination and fragmentation of nearshore, shallow‐water habitats through dredging, filling and hardening of shorelines that often are prime nurseries for the development and 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
