Australian coastal species are diverse with high rates of endemism, and include iconic plants and animals to which many Australians feel a strong connection. Charismatic coastal species such as crocodiles and dugongs captivate the minds of many Australians, and therefore contribute to our wellbeing through the appreciation of nature. Coastal species are an important part of marine ecosystems, with diverse cultural, social and livelihood values for Traditional Owners (Skewes et al. 2012, Smyth et al. 2018). Traditional Owners have contributed to valuing the importance of coastal species (Butler et al. 2012, Johnson et al. 2018, Smyth et al. 2018), although this practice is not widely adopted across the nation. A more common practice involves Traditional Owners monitoring coastal species through their Indigenous Land and Sea Ranger programs, which often informs local management and planning (see the Indigenous chapter). The statuses of some coastal species feed into indicators of change. Assessment The condition of coastal species 2021 Adequate confidence Indigenous assessment Threatened species, particularly shorebirds, are in poor and declining condition. This is mostly due to degradation of their habitats near the coast, both within Australia and (for migratory species) overseas. Fishes and invertebrates in bays and estuaries are also considered to be in poor condition. In contrast, crocodile populations are healthy and growing, and dugongs are in good and stable condition. The Indigenous assessments for the state of coastal species found 1 asset is poor, 3 are good and 1 is very good, and the trend is deteriorating for 1 asset, unclear for 2 and stable for 2. Local government assessments (see Approach) showed threatened species and shorebirds to be in poor condition in most parts of Australia, but particularly near capital cities. Related to United Nations Sustainable Development Goal targets 14.2, 14.4, 14.5, 15.5 Legend How was this assessment made Share on Twitter Share on Facebook Share on Linkedin Share this link Assessment Threatened species 2021 Adequate confidence More than half of all threatened species are found in the coastal zone and are concentrated near urban centres, where threats are greatest. The Indigenous assessment for some regional areas was poor, with a deteriorating trend. Assessment Shorebirds 2021 Adequate confidence 2016 Shorebirds are in severe, ongoing decline due to critical habitat loss in Australia and Asia, compounded by the impact of other threats. The Indigenous assessment for some regional areas was good, with a stable trend. Assessment Crocodiles 2021 Adequate confidence 2016 Crocodiles are thriving in the Northern Territory and parts of Queensland. The Indigenous assessment for some local areas was very good, with a stable trend. Assessment Dugongs 2021 Somewhat adequate confidence 2016 Dugongs are in good condition in northern Australia, though threatened by habitat loss in south-eastern Queensland. The Indigenous assessment for some regional areas was good, with an unclear trend. Assessment Fishes in estuaries and bays 2021 Limited confidence 2016 Diversity and abundance of fish assemblages in estuaries and bays are altered by declining water and habitat quality associated with increasing human activities and climate change impacts. The Indigenous assessment for some local areas was good, with a stable trend. Assessment Invertebrates in estuaries and bays 2021 Limited confidence 2016 Biodiversity is probably declining, depending on coastal development, invasive species and climate change, but confidence is low due to lack of monitoring. The Indigenous assessment for some regional areas was good, with an unclear trend. Threatened species The density of threatened species around Australia’s coastline is an important indicator of human impacts on native biota and the status of these species. According to the latest (2019) data on threatened species listed under the federal Environment Protection and Biodiversity Conservation Act 1999 (EPBC Act) (DAWE 2019), 1,010 threatened species (56% of all listed species) are found within the coastal zone (i.e. within 50 kilometres (km) inland of the coastline). The highest density of threatened species is found along the eastern coast of Australia, particularly around the urban centres of Brisbane, Cairns, Melbourne and Sydney (Figure 17). Figure 17 EPBC-listed species richness within 50 kilometres of the coastline Expand View Figure 17 EPBC-listed species richness within 50 kilometres of the coastline EPBC = Environment Protection and Biodiversity Conservation Act 1999 Note: Each species distribution was intersected with a 5 km2 grid of the coastal region, and a count for each grid cell was calculated. Share on Twitter Share on Facebook Share on Linkedin Share this link Other areas of high density of threatened species are eastern Australia between Sydney and Brisbane, the north-eastern coast of Tasmania, the Northern Territory around Darwin, and isolated pockets of south-western Western Australia. Patterns in threatened species density are correlated with human population density, but the factors affecting threatened species along Australia’s coastline are highly variable. There are now 21 key threatening processes affecting threatened species listed in the EPBC Act, and the recent analysis by Ward and colleagues (Ward et al. 2021) shows that there are 48 distinct threatening issues (Figure 18). Threatened species found within Australia’s coastal regions are most often imperilled by the impact of invasive weeds (n = 328, or 32% of all threatened species in the coastal zone), but there are also many species affected by habitat loss driven by the agriculture and aquaculture sector (n = 218, or 21%). Broad-level threatening processes associated with habitat loss, fragmentation and degradation, invasive species and disease, and adverse fire regimes are impacting over 94% of coastal threatened species (Figure 18). Even in remote areas of Australia, such as the southern and northern coast, there are threatened species. There is now clear evidence of cumulative pressures in these once-remote areas, including invasive species (e.g. cane toads and cats affecting northern reptiles and mammals), fires impacting plant species and overseas pressures on migratory shorebirds (see the Biodiversity chapter). Figure 18 Number of threatened Australian taxa within the coastal region and relative level of impact for each subcategory threat, nested within the corresponding broad-level threat class Expand View Figure 18 Number of threatened Australian taxa within the coastal region and relative level of impact for each subcategory threat, nested within the corresponding broad-level threat class Share on Twitter Share on Facebook Share on Linkedin Share this link Shorebirds Australia has 64 ‘core’ populations of shorebirds. Around one-third of these depend on coasts for their life cycles (‘coastal obligates’) when in Australia, and almost half use the coast in a substantial way. Detailed population trend analyses since 2016, and the listing of threatened populations, show that previous assessments of the condition of shorebirds were likely over-optimistic. Australia appears to be losing its migratory shorebirds, largely driven by habitat loss in Australia and overseas, climate change, and the interaction between these, plus local pressures. All key threats to shorebirds – residents or migrants – remain or have intensified since 2016. Shorebird population trends Since 2016, the evidence base for assessing trends and conservation status of shorebirds has increased dramatically. Revised population estimates (Hansen et al. 2016) and major trend analyses of shorebirds have recently been published, some 50 years since national shorebird monitoring began (Fuller et al. 2020). Monitoring is concentrated at coastal sites and reveals continental-scale decreases in numbers of 12 of 19 migratory shorebird species (17 of 19 for southern Australia) between 1973 and 2014 (Clemens et al. 2016). Three coastal-resident species exhibited stable population trends over this period (Clemens et al. 2016). Under the EPBC Act, 4 Australian shorebird populations are regarded as Critically Endangered, 5 as Endangered and 3 as Vulnerable. These populations have all been listed since the 2016 state of the environment report, as the trend analyses became available (Figure 19). Four additional populations that occur in Australia are listed globally as Near Threatened on the International Union for Conservation of Nature Red List. Australia’s shorebird species are increasingly recognised as being threatened (currently 19% of 64 core Australian populations are threatened; most of these use Australia’s coasts). Figure 19 EPBC Act–listed shorebird species in Australia, 2000 to 2021 Expand View Figure 19 EPBC Act–listed shorebird species in Australia, 2000 to 2021 EPBC Act = Environment Protection and Biodiversity Conservation Act 1999 Share on Twitter Share on Facebook Share on Linkedin Share this link Pressures on shorebirds Habitat loss is one of the main pressures affecting shorebirds, but the largest habitat losses occur outside Australia. Population declines in migratory species are widespread throughout Australia and are especially pronounced in the south. These declines are consistent with habitat loss and degradation in the East Asian–Australasian Flyway (Clemens et al. 2016, Studds et al. 2017), where major land reclamation has affected estuaries and coastal wetlands (Moores et al. 2016, Lee et al. 2018). Habitat loss is particularly rapid and extensive in the Yellow Sea, where habitat has declined for some populations by up to 1.7% per year (Murray et al. 2018). Reduced survival of individuals migrating through the Yellow Sea drives decreases in Australian populations of several shorebird species (Piersma et al. 2016, Dhanjal‐Adams et al. 2019, Adams et al. 2020a). The climate of northern hemisphere breeding grounds has also been linked to the abundance of some populations in Australia (Murray et al. 2018, Dhanjal‐Adams et al. 2019). Species that rely on the Yellow Sea are more sensitive to climate anomalies and are also more likely to be declining in Australia, suggesting that resilience to climatic challenges may be compromised by habitat loss (Wauchope et al. 2017, Dhanjal‐Adams et al. 2019). Sea level rise is forecast to cause considerable habitat loss, and to impact some species more than others depending on their migration routes (Iwamura et al. 2013). Shorebird species that use both coastal and inland wetlands in Australia may also be impacted by loss of inland wetlands due to increasingly frequent drought and water extraction; there is some evidence that survival of these species decreases in drought years when less habitat is available inland (Clemens et al. 2021). In Australia, existing pressures are extensive, expanding, ongoing and intensifying. These pressures include coastal development, water diversion, pollution, disturbance (physical disturbance, disruption of normal shorebird activities through the presence of people, noise, and artificial light at night), inappropriate pet management and altered predator regimes. Climate change is likely to alter predator–prey dynamics, which affect shorebird nesting success (Kubelka et al. 2018). The impacts of climate change are also affecting Australian coastal tropical and temperate wetlands in ways likely to affect shorebirds (Saintilan et al. 2019). Other issues affecting shorebirds have emerged since 2016, including an increase in the use of horses on some coastlines, and harvesting of kelp on ocean beaches (PIRSA Fisheries and Aquaculture 2015). There are, however, a handful of successful site or species management stories. For example, the decline of the hooded plover (Thinornis rubricollis) has stabilised in parts of its range where intensive management has occurred, although the species continues to decline elsewhere and requires ongoing management to consolidate gains. Shorebirds in coastal Australia rely heavily on artificial habitats such as saltworks and sewage treatment plants, and sympathetic management of these areas is likely to be critical to maintaining shorebird populations (Jackson et al. 2020, Jackson et al. 2021). Appropriate management of environmental water allocations is also paramount, as these are important to some near-coastal wetlands such as the Coorong in South Australia (see Flow regimes), and many coastal populations of shorebirds use, and therefore depend upon, inland wetlands also (Clemens et al. 2021). Threats to migratory shorebirds in Australian shorebird sites range from low to extreme, given wide variation in exposure to human activity, the degree to which they are protected and the condition of available habitat. Spatially explicit mapping of threats and shorebird site usage offers a systematic approach to management (Lisson et al. 2017), but is not yet widely available. Crocodiles Australia has 2 species of crocodile: the saltwater crocodile (Crocodylus porosus), which inhabits saltwater habitats and brackish estuaries, and the freshwater crocodile (C. johnstoni), which inhabits inland rivers, swamps and other water bodies (Webb et al. 1983) and is found only in Australia. Saltwater crocodiles were protected in 1971 and since then most populations have increased, though this varies between regions. Freshwater crocodile populations are, however, declining in the Northern Territory. Saltwater crocodiles In the Northern Territory, habitats for the saltwater crocodile include numerous tidal rivers and creeks, floodplains, billabongs, and freshwater swamps, and most of these remain relatively intact (Fukuda et al. 2007, Fukuda & Cuff 2013). These habitats extend along the coastline (around 11,000 km) and tidal rivers (typically 100–200 km inland). As in the Northern Territory, habitats for C. porosus in Western Australia are relatively intact and occur in areas with a very low human population. Major crocodile populations in Western Australia are within protected areas. In contrast, crocodiles in Queensland exist from the coast to far inland, and occupy a far more diverse range of habitat types (13 defined crocodile bioregions), most of which are considered marginal or suboptimal for crocodiles (Taplin 1987). The Queensland crocodile population is primarily riverine, with over 90% found below 20 m elevation (Taplin 1987, Read et al. 2005, Taplin et al. 2020). On the eastern coast of Queensland, there is a relatively high human population and there has been significant habitat alteration for agriculture (Taplin 1987, Read et al. 2005). In the Northern Territory, 12 C. porosus populations in selected rivers have been monitored since their protection in 1971 (Messel et al. 1981) (Figure 20). All of the rivers have shown significant increases in the number and biomass of crocodiles (Fukuda et al. 2011), although the rate of increase in many rivers has slowed significantly in recent years (Saalfeld et al. 2016). This suggests that populations are approaching their habitat’s carrying capacity, which varies river by river depending on the resources available, such as nesting habitat (Fukuda et al. 2007). Indeed, some of the monitored rivers continue to show an increase in biomass over time, with no sign of plateauing, suggesting that individuals are growing larger while the total number of crocodiles may have plateaued. In the Northern Territory, the current C. porosus population is estimated to be around 100,000 individuals (excluding hatchlings) (Fukuda et al. 2021), and sustains a commercial harvest of up to 90,000 eggs and 1,200 crocodiles annually across the Northern Territory (except for the Kakadu National Park). This does not include the removal of 200–300 crocodiles annually as part of public safety programs (Fukuda et al. 2014). In Queensland, population monitoring of C. porosus has been relatively sporadic and inconsistent over time, with statewide surveys in the late 1980s, 1990s and recently in 2016–19. Although the C. porosus population in Queensland has increased since the 1980s, recovery has been relatively slow and highly variable across the state, at an average of around 2% each year (Taplin 1987, Read et al. 2005). While numbers in some rivers appear to have stabilised as early as the 1980s (e.g. Wenlock River, north-western Cape York), in other rivers (e.g. Norman River, Gulf of Carpentaria) numbers continue to increase (Taplin 1987, Read et al. 2005, Taplin et al. 2020). The current C. porosus population in Queensland is estimated to be 20–30,000 individuals (excluding hatchlings), with an average density of 1 crocodile per kilometre of river surveyed (Taplin et al. 2020). It only became lawful to harvest wild saltwater crocodile eggs in Queensland in 2018 under the Nature Conservation (Estuarine Crocodile) Conservation Plan 2018, with only one group currently permitted to collect in the Pormpuraaw region. Over the past 10 years, around 450 problem crocodiles have been removed for management purposes in Queensland (Taplin et al. 2020). Very low numbers of problem C. porosus have been removed in Western Australia over the past 30 years. In Western Australia, historical population monitoring of saltwater crocodiles was based on annual aerial surveys in Cambridge Gulf (Ord River, West Arm), with spotlight surveys carried out less regularly in some areas (Mawson 2004). Currently, regular monitoring is restricted to an annual spotlight survey of the King River, which has been surveyed in most years since 1989 (Corey et al. 2020). Legal harvesting of juveniles, sub-adults, adults and eggs was undertaken in West Arm between 1989 and 1994 to provide stock for crocodile farms. Since cessation of harvesting, the most recent surveys indicate relatively high rates of increase in C. porosus populations in West Arm (4.1% per year in 2008), the tidal Ord River (6.9% per year in 2008), the nontidal Ord River (4.7% per year in 2019) and King River (3.3% per year in 2020) (Webb et al. 2010, Corey et al. 2020), with no sign yet of stabilising. In 2015, spotlight surveys of the Prince Regent, Hunter and Roe rivers confirmed healthy breeding populations, and a 300% increase in abundance since 1970 (Parke 2015). Cattle grazing is a potential threat to some nesting habitats. Figure 20 Saltwater crocodile (Crocodylus porosus) populations in monitored rivers in the Northern Territory since 1971 Expand View Figure 20 Saltwater crocodile (Crocodylus porosus) populations in monitored rivers in the Northern Territory since 1971 km = kilometre Share on Twitter Share on Facebook Share on Linkedin Share this link Freshwater crocodiles The Australian freshwater crocodile is not currently subject to major commercial harvest and safety programs (Delaney et al. 2010). In 1987, the population in the Northern Territory was estimated to be 30,000–60,000 individuals (excluding hatchlings) (Webb et al. 1983), but this decreased considerably after the 1990s because of invasive cane toads (Bufo marinus), which can poison crocodiles when consumed (Fukuda et al. 2016). Populations in 2 river systems have been monitored since the 1980s and all have shown consistent and significant declines since the early 2000s, coinciding with the arrival of cane toads. Detailed analyses in one of the monitored rivers (Daly River) revealed that the total number of crocodiles declined by 70% between 1997 and 2013, with small (0.6–1.2 m) individuals most severely affected (Fukuda et al. 2016). Despite increasing concern, the invasion of cane toads is seemingly irreversible and no adaptive management has been effective, except for continued monitoring surveys. In Queensland, no recent population studies have been conducted on C. johnstoni, so the population size remains unquantified (Read et al. 2005). However, incidental observations from 2016–19 indicate the species remains common. While the impact of cane toads on the C. johnstoni population in Queensland is unknown, the species remains widespread and abundant, suggesting the species has the potential to adapt to and endure impacts from cane toads. In Western Australia, the C. johnstoni population in the Fitzroy and Ord rivers, Lake Argyle and Lake Kununurra was estimated to be at least 47,000 individuals (McNamara & Wyre 1992). Helicopter count surveys over 1996–2012 indicated that the populations in Lake Argyle and Lake Kununurra were increasing at around 8% per year, despite some impacts of catfish fisheries (WMI 2012). Numbers in the upstream Ord River have decreased since 2008, which is considered to be the result of increasing numbers of larger C. porosus moving upstream (WMI 2019). Unlike the Northern Territory, in Western Australia C. johnstoni populations do not appear to have been impacted significantly by the arrival of cane toads in 2009 (Somaweera & Shine 2012, Clarke et al. 2020). Dugongs The biodiversity values and cultural importance of the dugong (Dugong dugon) are exceptional. One of 4 living species in the mammalian order Sirenia and the only living species in the family Dugonidae, the dugong is the only herbivorous mammal that is strictly marine. The dugong is a cultural keystone species for some Indigenous people living within its Australian range (Butler et al. 2012). The Australian dugong population is the largest population in the world, with their range stretching from Shark Bay in Western Australia to Moreton Bay in Queensland. The dugong is explicitly mentioned in the statements of Outstanding Universal Value of 2 World Heritage Areas: Shark Bay and the Great Barrier Reef (Figure 21). The species is designated as a Matter of National Environmental Significance and is protected under the EPBC Act as a listed migratory and marine species. The dugong is listed as Other Specially Protected Fauna in Western Australia and Vulnerable in Queensland. The outlook for dugongs in the Southern Great Barrier Reef (Queensland) is poor (Figure 21). The outlook in the remainder of the species’ range appears to be good in the short term, but is likely to deteriorate in the long term if there is further development in the remote north of Australia, or if seagrass meadows and dugong demography and health are significantly affected by climate change. Dugong populations The dugong is the most abundant marine mammal in the coastal waters of northern Australia (Marsh et al. 2011). Standardised aerial surveys provide data on the distribution and abundance of the dugong population in Australia. These surveys show that the conservation status of the dugong is uneven across its Australian range (Figure 21); however, confidence in this assessment varies because of regional and temporal differences in survey methodology and frequency. The main threat to dugongs is loss of seagrass habitat associated with extreme weather events, especially floods, cyclones and marine heatwaves. Habitat loss reduces recruitment (addition of new individuals to the population) with a 1.5- to 2-year lag (Fuentes et al. 2016, Bayliss et al. 2018). Recruitment (proportion of sightings that are attendant calves) is a robust index of population health. Survival following large-scale seagrass loss relies on having alternative habitat to move to, which emphasises the potential effects of cumulative impacts on multiple habitat areas (Gales et al. 2004). Habitat loss is also associated with increased mortality of individuals at the end of winter (Meager & Limpus 2014). Important Marine Mammal Areas (IMMAs) are defined as discrete portions of habitat important to marine mammal species, and can be delineated and managed for conservation (Di Sciara et al. 2016). In 2020, 12 IMMAs with dugongs as a qualifying species were identified in Australian waters (Figure 22). The rate of change in dugong populations is most sensitive to adult mortality (Marsh et al. 2012). Initiatives to reduce direct mortalities are most developed on the eastern coast of Queensland and in the Torres Strait. Initiatives include the Torres Strait Dugong Sanctuary; commercial fisheries closures, especially closures to gillnetting; localised initiatives to reduce the risk of vessel strike; and agreements with Traditional Owners (Marsh et al. 2012, Marsh et al. 2020). The incidence of unreported incidental catch in commercial gillnets in Queensland and the Northern Territory is unknown because of inadequate surveillance. Information on dugong abundance and distribution is important to support management of this species. However, surveys of dugong populations reflect jurisdictional rather than bioregional or genetic boundaries, and survey timing is not coordinated for temporal consistency. New methods have been developed to address the detection biases associated with aerial surveys (Pollock et al. 2006, Hagihara et al. 2014, Hagihara et al. 2018), with some methods able to correct for water depth as well as environmental conditions (Hagihara et al. 2014, Hagihara et al. 2018). This is especially important in the Torres Strait, where a high proportion of sightings are in deeper water; the latest population estimates for Torres Strait are consequently many times higher than previous estimates. The most robust trend data are from the eastern coast, south of 10°S, where Bayesian statistics have been used to detect trends (Marsh et al. 2019). Figure 21 Range map showing the latest estimates of dugong population size and trends of various components of the dugong population in Australia Expand View Figure 21 Range map showing the latest estimates of dugong population size and trends of various components of the dugong population in Australia GBR = Great Barrier Reef; NT = Northern Territory; QLD = Queensland Note: Produced by Adele Edwards from information collated by Helene Marsh. Data sources included aerial surveys conducted using the Pollock et al. (2006) method, and the method of Hagihara (Hagihara et al. 2014, Hagihara et al. 2018). Baseline: trend unavailable or low confidence. The trend assessment for Shark Bay (Bayliss et al. 2018) and the Gulf of Carpentaria coast of the Northern Territory Northern Territory (Griffiths et al. 2020) are based on frequentist statistics. The assessment for Torres Strait is based on several lines of evidence (Marsh et al. 2015), but recent Traditional Owner observations are generally consistent with widespread seagrass dieback, which is likely to have adverse impacts on the dugong population; those for the east coast locations are based on data from Sobtzick et al. (2017), Marsh et al. (2020) and unpublished work by Marsh and Rankin. Share on Twitter Share on Facebook Share on Linkedin Share this link Figure 22 Important Marine Mammal Areas in Australian waters for which the dugong is a qualifying species, identified by an expert workshop in 2020 Expand View Figure 22 Important Marine Mammal Areas in Australian waters for which the dugong is a qualifying species, identified by an expert workshop in 2020 Share on Twitter Share on Facebook Share on Linkedin Share this link Fishes in estuaries and bays Estuaries and coastal bays are highly productive environments and play a key role in the life history of fishes. In addition to supporting resident communities, estuaries provide essential nursery grounds, migration routes, and refuge and feeding opportunities for many fish species, including those of high commercial, recreational or conservation value. Fishes in estuaries and bays are threatened by the combined action of local human activities; habitat loss due to urban, agricultural and industrial developments (e.g. land reclamation); and climate change (Warwick et al. 2018, Gillanders et al. 2022). Contamination by legacy (e.g. heavy metals) and emerging contaminants (e.g. pharmaceuticals, microplastics, perfluoroalkyl substances) is a pervasive threat, particularly in systems adjacent to urban and industrial areas (Taylor et al. 2018, Anim et al. 2020). Commercial and recreational fishery pressure is often higher in estuaries near population centres (Taylor & Suthers 2021) (see the Marine chapter). Estuarine fish populations remain in poor condition and are faced with escalating pressures from climate change, coastal urbanisation, and increased population density and recreational fishing (Taylor & Suthers 2021, Gillanders et al. 2022). Resource-sharing strategies among stakeholders can ameliorate population density issues to some degree, but recreational fishing is difficult to manage (see the Marine chapter). Developing monitoring and management strategies will be key to evaluating impacts and to providing a robust evaluation of trends in the condition of fishes in estuaries and bays. Despite catch data from commercially targeted and managed fisheries, we still lack long-term fisheries-independent data and assessments of fish species that depend on estuaries, and data on recreational catch and effort. For example, there are gaps in our understanding of nursery use, estuarine contributions to coastal populations, the role of estuarine conditions, and impacts of environmental change across the distribution of breams (Acanthopagrus australis, A. butcheri) and mulloway (Argyrosomus japonicus). Diver surveys conducted by Reef Life Survey provide data on reef fish abundance in several bays and estuaries around Australia, some of which show change in species composition indicative of effects of climate change (see case study: Australia’s changing reefs, in the Reef recovery and management section in the Marine chapter). Impacts of environmental change on fishes in estuaries and bays depend on climate and local processes. The underlying factors differ among tropical and temperate bioregions, and the highly variable nature of closed and open coastal lagoons can make it difficult to detect long-term trends. In temperate Australian estuaries, increased temperatures, exacerbated by reductions in precipitation and riverflow, lead to poor environmental conditions, jeopardise ecosystem function, and can change fish assemblage dynamics and species dominance (Williams et al. 2017, Hallett et al. 2018, Gillanders et al. 2022). In New South Wales, drought has contributed to declines in catch rates of commercial species (Gillson et al. 2009, Stewart et al. 2020). In the Coorong (South Australia), and many systems along the south-western coast (Western Australia), declining water quality associated with hypersalinity, stratification, eutrophication (excess nutrients) and hypoxic (low oxygen) events impact fish diversity and abundance (Ferguson et al. 2013, Hallett et al. 2016c). Physiological stress has impacts on growth, condition and ultimately fish survival (Hossain et al. 2016, Cottingham et al. 2018). Many systems in temperate Australia are small, shallow, and have only temporary connections with the ocean. With climate change and upstream water abstraction, closure periods are increasing in frequency and duration, along with increasing severity of hypersalinity and low oxygen events (Hallett et al. 2018, Scanes et al. 2020a). Connectivity to the ocean is also reduced, affecting migratory movements, estuarine spawning and larval supply (Ye et al. 2017, Hoeksema et al. 2018). Thus, opportunities for population recovery are few, increasing the likelihood of local extirpations. In tropical areas, the timing and magnitude of rainfall between wet and dry seasons drive changes in fish assemblages. In addition to impacts from changing flow regimes associated with climate change or human intervention, there is concern about harmful dissolved oxygen dynamics, and how this might limit fish habitat use and estuarine nursery function (Dubuc et al. 2017, Wong et al. 2018). Because fish diversity and abundance increases with proximity to structurally complex habitats (Henderson et al. 2019), mangrove dieback and disturbances to seagrass and saltmarshes also threaten fish populations (Duke 2017). This is particularly because the benefits of these habitats extend beyond their edges and include supporting broad food webs (Gilby et al. 2018, Jinks et al. 2020). Understanding how environmental, geomorphological and local factors interact to determine fish populations in bays and estuaries is essential (Bradley et al. 2019). Changes in riverflow and restrictions to connectivity between estuaries and the coastal ocean have far-reaching consequences. The importance of estuarine habitat mosaics and maximising seascape connectivity should be recognised and translated into management and restoration strategies (Bradley et al. 2019, Marley et al. 2020), such as artificial reefs (Folpp et al. 2020) and restocking with hatchery-reared fingerlings (Taylor & Suthers 2021). Seagrass-friendly boat mooring and the development of citizen science programs to restore key fish habitats in urbanised estuaries are other potential management actions to enhance or restore fish populations (Marzinelli et al. 2016). Management strategies should also consider predicted changes to oceanographic processes and coastal winds, which will affect larval transport along the coast to estuarine habitats (Schilling et al. 2020, Schilling et al. 2022). Invertebrates in estuaries and bays The invertebrate fauna of Australian estuaries and bays are diverse and abundant, and play a critical role in ecosystem functioning. They recycle nutrients through the food chain, disturb and oxygenate sediment, and maintain water quality by filtering particles from the water column. They are also an important food source at various levels of the food web, including for fish and wading birds, and include commercially important crustaceans and molluscs. However, this role means that they can also facilitate the transfer of contaminants, such as heavy metals and pesticides, through the food web and potentially to humans (Jahan & Strezov 2019). Invertebrate fauna exist in a variety of life forms and living modes, including species that: are firmly attached to hard substrates; these include sponges, ascidians, molluscs (gastropods, bivalves), lace corals (bryozoans) and calcareous tube worms (serpulid polychaetes) are errant – they live among attached animals or are hidden in attached algae; these include such as crabs, shrimps and echinoderms burrow into soft sediments; these include nematodes, polychaetes, amphipods and isopods live on blades of seagrasses, among kelp holdfast, or on mangrove trunks or pneumatophores; these include polychaetes, hydroids and micromolluscs form their own calcareous or sandy reefs; these include sabellariids and serpulid polychaetes. Most invertebrate fauna have specific habitat requirements and geographical distributions. Species distributions vary around Australia, with distributions better known in temperate than tropical regions. However, even in temperate regions, a considerable proportion of the fauna still remains to be described, and, in some cases, species are being found that represent suites of undescribed species (Zanol et al. 2016, Zanol et al. 2020). Human impacts on invertebrates Invertebrates are strongly impacted by coastal development. Modification of their habitat is increasing with coastal development, and catchment factors such as land run-off, eutrophication and sedimentation all carry potential impacts. These pressures vary in intensity around the coast but are greatest in urbanised estuaries. Invertebrate populations are almost certainly changing in diversity and abundance, and there have likely been local extinctions in developed areas (Cole et al. 2017). However, long-term datasets and monitoring programs are almost non-existent, apart from those for commercially valued or harvested species, and detection of impacts is hampered by natural fluctuations in species abundances and diversity (Hutchings & Jacoby 1994, Gladstone et al. 2020). Bays and estuaries are subject to both commercial and recreational fishing for molluscs and crustaceans. Although bait-collecting of mud worms is allowed only within bag limits (Cole et al. 2018), this is managed as if only one species is being caught, whereas in many places several species are involved and these species may differ in breeding patterns and habitat requirements. Collecting may also lead to habitat destruction, because some species live in seagrass beds. Similar issues also apply to pumping for nippers (burrowing shrimp). Populations of commercially important crab species, such as blue swimmer and mud crabs, can be affected by degradation of seagrass beds and mangrove habitats, as can populations of prawns with larval stages that use these habitats. Impacts from climate change include increasing water and air temperatures, changes in rainfall and therefore salinity, changes to water currents affecting larval recruitment, rising sea levels, increased storm activity, and ocean acidification. The extensive drought (2017–2019) in eastern Australia would have reduced freshwater run-off into bays, estuaries and coastal lagoons, and in some cases led to increasing salinities with increased rates of evaporation. Invasive species, such as the seaweed Caulerpa taxifolia, European green crab (Carcinus maenas) and the northern Pacific seastar (Asterias amurensis), continue to impact native species in bays and estuaries (Ross et al. 2002, Thresher et al. 2003, Gribben et al. 2013). This highlights the need for ongoing marine biosecurity for both national and international vessels, and the need to accurately identify new introductions and distinguish them from native or as-yet-undescribed native species (Kupriyanova et al. 2016). There are emerging threats that are likely to impact invertebrates, but these require further study. Run-off from burnt forests into bays and estuaries (e.g. during the devastating bushfires of 2019–20) almost certainly causes eutrophication and reduced oxygen levels. In areas where fire retardants have been used, run-off from rains after the fires may have also affected invertebrates. Given that some molluscs only occur in particular catchments, these stressors may have resulted in local extinctions (Ponder 2003). Although, on the whole, pressures to invertebrates are increasing, there are some notable examples of recovery following implementation of effective management strategies at large scale. For example, coincident with bans on tributyltin antifouling paints, oysters have returned to Sydney Harbour (Birch et al. 2013, Birch et al. 2014). Restoration and rehabilitation projects focused on reinstatement of habitat-forming species may lead to localised increases in the abundance of some species, and monitoring and evaluation programs are needed to assess the benefits of these projects over ecologically and environmentally relevant timescales.