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Fishes that are estuary‐dependent in the egg, larval and juvenile stages often encounter major changes in their environment as they undertake ontogenetic migrations. Early‐life stages of estuary‐dependent and ‐associated fishes are more likely to experience a broader range of environmental variability in shallow estuaries than marine fishes on continental shelves or in the open sea. Accordingly, early‐life stages must be adaptive or tolerant, for example, to shifting environmental conditions. Amongst the most important environmental factors are (i) temperature, (ii) precipitation and associated freshwater flow, (iii) salinity, (iv) measures of estuarine productivity, including prey resources, and (v) water quality, e.g. dissolved oxygen and pH. Within the estuary, environmental factors may act chronically or as episodic events (Houde 1989b) to control survival and growth of eggs and larvae or, in the longer term, to modulate production, particularly of juveniles in the weeks or months of extended, young‐of‐the‐year stages. Environmental factors that are threats to reproduction and recruitment, beyond causing usual variability, are addressed in Section 3.5. As one example, hypoxia is sometimes common in estuaries and may be a chronic stressor or an episodic threat to production and recruitment; it can also hinder or prevent migrations by adult spawners or early‐life stages through estuarine hypoxic zones (Breitburg 2002, Breitburg et al. 2018, Able et al. 2022).

Temperature is often the most important variable affecting growth and survival of estuarine fish larvae (e.g. Rutherford & Houde 1995, Morongiello et al. 2014, Houde 2016). For example, in the Baltic Sea, temperatures above the physiological optimum were found to reduce survival of larval Clupea harengus (Arula et al. 2016). Further, decreasing larval growth rates and productivity of larvae occurred at temperatures >17 °C, a level that has occurred frequently in the past decade (Moyano et al. 2020). A thermal threshold index for the Baltic Sea, based on the number of days above optimal 16 °C during the spawning season (March–June) has increased in recent decades. Growth rates and postlarval abundance of the estuary‐dependent sillaginid Sillaginodes punctata are strongly and positively related to temperature (correlation >0.80) for larvae that ingress from offshore Australian waters to Port Phillip Bay (Figure 3.14). Recruitment outcomes for S. punctata are determined by temperature and offshore transport that is most favourable at relatively high temperatures (Jenkins & King 2006). In North American estuaries, low temperatures during winter threaten recruitment success of some fishes, e.g. the sciaenid Micropogonias undulatus (Hare & Able 2007, Hare et al. 2010) and the scophthalmid Scophthalmus aquosus (Neuman & Able 2003).

Figure 3.14 Growth rates (mean otolith increment widths, open circles) of larval stages of the sillaginid Sillaginodes punctata sampled after ingress to Port Phillip Bay, Australia, and postlarval abundances (closed circles) in 1998–2003 showing the strong correspondence between growth rate and abundance. Spawning by S. punctata occurs in the coastal ocean and larval growth rates are strongly related to temperature

(from Jenkins & King 2006, their figure 3).

Reviewing literature on factors affecting recruitments of estuary‐associated fishes, Martinho et al. (2012) reported that temperature and river flow were amongst the best predictors of recruitment potential of estuarine fishes. Levels of river flows usually were positively related to recruitment success. As examples, the moronid Morone saxatilis in Chesapeake Bay (Martino & Houde 2012) and the percichthyid Percalates colonorum in Australia (Morongiello et al. 2014) experience better recruitment under conditions of elevated precipitation and river discharge. However, effects of freshwater flow may be negative for other species (e.g. Ramos et al. 2006). Very high flows in small South African estuaries result in temporarily reduced abundances of recruiting marine (Whitfield & Harrison 2003) and estuarine‐resident species (Strydom et al. 2002). In the lateolabracid Lateolabrax japonicus, exceptionally high levels of river discharge reduce its recruitment levels in the Ariake Sea‐Chikugo River (Japan) estuary (Shoji et al. 2006). Other factors may interact with flow and precipitation. For example, larval recruitment of the pleuronectid Platichthys flesus to the Lima Estuary (Portugal) was strongly negatively related to coastal sea‐surface temperature, positively related to coastal chl‐a and weakly but positively related to precipitation and freshwater flow (Amorim et al. 2016).

In salmonids, temperature, dissolved oxygen and precipitation are three factors frequently identified as exercising control over early‐life survival and recruitment. Salmonids provide exceptional examples due to their unique early‐life history. For these anadromous fishes, most mortality occurs during the period when the eggs and/or fry are buried in their gravel nests (redds) in freshwaters above estuaries (Quinn 2018). Several responses are clear. First, the rate of embryonic and fry development is clearly temperature dependent (Quinn 2018). For example, the number of days to hatch and the days to emergence from the gravel nest depend on temperature and vary with species. In some instances, extreme high or low temperatures can be lethal. Second, dissolved oxygen can influence survival, with lower levels a frequent source of mortality. This can occur when groundwater has lower levels of dissolved oxygen than surface waters (Quinn 2018). Furthermore, if interstitial spaces in the redd are filled with fine silts, the flow of oxygenated water is reduced (Peterson & Quinn 1996), which is particularly important because the time from egg to fry emergence in salmonids can range from weeks to months, during which time eggs and embryos can be susceptible to stress from low dissolved oxygen. Moreover, the oxygen demand increases during embryonic development (Quinn 2018). Thirdly, scouring of nests by high water currents, often closely tied to levels of precipitation, may displace embryos, exposing them to predators and other sources of mortality (Quinn 2018).

Air temperature during late winter is the primary environmental indicator of recruitment variability in spring‐spawning Clupea harengus in the Baltic Sea. Winter‐spring temperatures and other climate variables exercise control during the period of highest larval mortality, mainly by controlling production of planktonic prey (Ojaveer et al. 2011). The dependence of recruitment on spawning stock biomass (SSB) varies amongst years with differing temperature conditions. In years of cold winters, environmental conditions are the dominant factor controlling year‐class abundance of C. harengus, and spawning stock biomass is not important. In milder winters, the importance of spawning stock biomass increases and is significantly related to recruitment success.

In another example, enhancement of anguillid eel recruitment under high‐flow conditions is especially evident for the glass‐eel stage of the catadromous Anguilla rostrata (Sullivan et al. 2006). Reduced freshwater discharge during droughts can diminish estuarine plumes and associated cues onto the continental shelf that may facilitate estuarine recruitment of fish larvae from offshore (Baptista et al. 2010). Some droughts can induce fish kills in estuarine nurseries, likely due to synergistic effects of hypoxia and resulting in diminished availability of food (Wetz et al. 2011). Effects of prolonged drought and its negative consequences for the nursery function and larval fish assemblages in the Murray‐Darling Estuary (Australia) have been documented (Bucater et al. 2013). Recruitments of pelagic fishes in the San Francisco Estuary (USA) are negatively impacted by years of prolonged drought (Sommers et al. 2007). Similarly, cessation of river flow into certain South African estuaries due to freshwater abstraction and the resultant loss of cues to the marine environment has been suggested as the major reason for reduced ingress and recruitment of estuary‐associated, marine postlarvae into such estuaries (Whitfield 1994).

Event‐scale weather can generate variability in recruitment success and may have more impact in estuaries (Stevens et al. 2006, Biggs et al. 2018, Massie et al. 2019) than in the ocean where effects of such events may be dampened, diluted and buffered by the large volume. In the moronid Morone saxatilis, major storms with high precipitation and excessive river discharges, often associated with temperature drops, may result in episodic, down‐estuary losses of eggs or larvae and temperature‐related mortalities in the Hudson River and Chesapeake Bay (Dey 1981, Rutherford et al. 1997). Sudden drops in water temperature (<14 °C) also cause mortalities of young fishes in tropical estuaries (Kyle 1989, Cyrus & McLean 1996). Storm‐related impacts do not always have negative outcomes. For example, there was no indication of increased mortality of the sciaenid Micropogonias undulatus larvae attributable to Hurricane Isabel in Chesapeake Bay; in fact, levels of ingress by M. undulatus larvae from offshore increased in the aftermath of this major storm (Houde et al. 2005, Montane & Austin 2005). Similarly, larval fish recruitment of certain species into the St Lucia estuarine system (South Africa) appeared to be enhanced following Cyclone Domoina (Forbes & Cyrus 1992). The effects of Hurricane Sandy on juvenile fishes in Barnegat Bay (USA) were not discernable despite annual sampling before and after the storm (Valenti et al. 2020).