Nationally, shorebird populations are in very poor condition and are rapidly deteriorating (Clemens et al. 2016). This is particularly true for species with a migration route passing through the Yellow Sea, where critical feeding areas have been lost (Murray et al. 2014). Four migratory shorebird species—the eastern curlew (Numenius madagascariensis), the curlew sandpiper (Calidris ferruginea), the great knot (Calidris tenuirostris) and the bar-tailed godwit (Limosa lapponica menzbieri)—are listed as critically endangered under the EPBC Act. There is broad agreement on the very poor state and trend of shorebirds, and consensus that the main causes are habitat loss and degradation, particularly in overseas areas on their migratory routes (Murray & Fuller 2015, Murray et al. 2015). Importantly, shorebird habitat can generally not be offset by other environmental compensation.
Pressures differ between resident and migratory shorebirds, and, consequently, so do their current states. Declines in resident shorebird abundances are attributed to coastal use and associated disturbance, with recreational pursuits, dogs, 4WDs and horses all adversely affecting shorebirds. The fitness and reproductive success of resident shorebirds are also reduced by introduced predators, and habitat loss and disturbance. There is evidence that degradation of inland wetlands in Australia, including from river regulation and abstraction (Silke et al. 2008), is affecting inland nonmigratory shorebirds, such as the red-necked avocet (Recurvirostra novaehollandiae), the black-winged stilt (Himantopus himantopus), the black-fronted dotterel (Elseyornis melanops) and the red-kneed dotterel (Erythrogonys cinctus) (Clemens et al. 2016). On a national scale, populations of nonmigratory coastal shorebirds are in better condition than those of migratory shorebirds (Clemens et al. 2016). However, there are cases where human activity on beaches is clearly placing pressure on individual shorebird populations, such as populations of the hooded plover (Thinornis cucullatus) across much of Victoria (Oldland et al. 2009), and the beach stone-curlew (Esacus magnirostris).
For migratory shorebirds, the dominant pressures are likely to be occurring overseas, and there is uncertainty about the degree to which human activities (e.g. urbanisation, water extraction) in Australia are contributing to their declines. However, nationally, feeding and roosting sites are deteriorating in extent and quality, limiting the ability of birds to make return flights to the Northern Hemisphere. Additionally, climate change, including sea level rise, threatens both coastal nonbreeding (Iwamura et al. 2013) and breeding (Wauchope et al. 2016) sites of shorebirds.
Shorebirds are declining in numbers, and threats are stable or increasing in most jurisdictions, although data on threats are limited, and it is difficult to distinguish between local and distant drivers of population decline. Many coastal areas in New South Wales are below the national average in retaining shorebird numbers, whereas in Western Australia, most shorebirds occur in the relatively pristine north-west. Populations in Victoria show variable trends, although some large areas are losing many shorebirds. In Queensland, there are many areas with large numbers of shorebirds (GBRMPA 2014), although data are insufficient, particularly in the north, to fully assess their population trends. At least 1 area in Queensland with sufficient data, Moreton Bay, appears to be doing worse than the national average.
In South Australia, the 2 largest shorebird areas—the Gulf St Vincent and the Coorong—are rapidly losing shorebirds, with local pressures deteriorating the condition of the Coorong and amplifying more broadscale impacts (Aharon-Rotman et al. 2016). Following a recent wet period, trends for some shorebirds in the Coorong have stabilised; however, this region is entering another dry spell (Paton & Bailey 2012). Gulf St Vincent is threatened by sea level rise and coastal development, although this may be mitigated by proposed protected areas. Trends in Tasmania are largely consistent with the national average, but some species are under severe threat. The once-abundant eastern curlew is now facing the very real risk of local extinction. Some analyses suggest that shorebird numbers are not declining in the Northern Territory, although most areas in the Northern Territory have too little data to assess.
Conservation can only be achieved if the whole suite of nesting, feeding and migratory habitats used by shorebirds are protected, including in their flyway to breeding areas in the Northern Hemisphere. Severe declines, mainly driven from overseas, make it all the more important that we effectively manage the shorebirds while they are here in Australia (Szabo et al. 2016). State and community groups have increased resident shorebird conservation efforts in recent years, such as hooded plover population restoration efforts in Victoria (Dowling & Weston 1999). With the possible exception of hunting in parts of Asia, no threat to shorebirds has been effectively managed in that region.
The short-term long-term outlook for shorebirds as a group is poor. Pressures in critical migratory staging sites in the Yellow Sea are increasing, along with habitat decline in some Australian areas, and sea level rise. Substantial conservation efforts are required to prevent further declines in resident shorebird populations. In the case of migratory shorebirds, these need to be coordinated with overseas programs.
Two species of crocodile are found in Australian coastal waters: the freshwater crocodile (Crocodylus johnstoni) and the saltwater crocodile (Crocodylus porosus). They are most abundant in the Northern Territory, and northern parts of Western Australia and Queensland, although there are increasing reports of sightings further south. In the past 5 years, there has been no sign of declines in saltwater crocodile populations, and their numbers continue to increase towards carrying capacity. Saltwater crocodiles were protected in Western Australia in 1970, in the Northern Territory in 1971 and in Queensland in 1974. Whereas saltwater crocodile numbers are improving, freshwater populations have remained stable since 2011 because some populations have been affected by cane toads.
A high proportion of Australian saltwater crocodiles are found in the Northern Territory, which has a comprehensive monitoring program in place. Regular survey data collected since shortly after protection in 1971 indicate that saltwater crocodile populations in the Northern Territory have achieved full recovery. They have returned to levels of abundance that existed before intensive hunting started in 1945, and average size and biomass are still increasing (Fukuda et al. 2011).
Reasonably consistent data from Western Australia indicate that saltwater crocodile populations are steadily but slowly recovering, but at rates slower than in the Northern Territory because habitats are not naturally optimal. Long-term monitoring of saltwater crocodiles in Western Australia is restricted to regions of the Kimberley. Population increases occurred between 2000 and 2012 in the Ord River, and between 1999 and 2005 in West Arm, following harvesting from 1985 to 1998. The West Arm population was stable between 2006 and 2012. As of 2015, populations in the Prince Regent, Roe and Hunter rivers had tripled in size during the past 30 years. In both Western Australia and the Northern Territory, human impacts from habitat destruction are minor.
Saltwater crocodiles in Queensland have increased in abundance since protection in 1974; however, survey data in Queensland are patchy and inconsistent and generally indicate slow recovery (Read et al. 2005). This is considered to be a result of a combination of the habitat being naturally unsuitable (insufficient breeding sites), extensive and ongoing habitat destruction because of coastal development and human population growth, and localised crocodile population depletion as a result of illegal shooting.
There is little concern for the outlook for saltwater crocodiles, in both the short and long terms, although increasing human–crocodile conflicts need to be addressed through appropriate management. Movement of saltwater crocodiles into upstream freshwater areas is an issue for both management and the displacement of freshwater crocodiles. Recently, calls have been made for culling of saltwater crocodiles to address growing public safety concerns. Saltwater crocodiles are increasingly used as a sustainable natural resource through tourism and farming in the Northern Territory and Western Australia, adding economic value to the species and assisting in their conservation. Similar commercial exploitation has been proposed in Queensland; however, there are questions about the science underpinning sustainable harvesting of these populations.
Monitoring of freshwater crocodiles is more limited than for saltwater crocodiles, but a few rivers in the Northern Territory have been closely monitored since the 1970s. The largest population in Australia occurs in the Daly River, Northern Territory, and data there show a serious decline in abundance during the past 15 years because of cane toads (Fukuda et al. 2015). Another large population is at Mary River, Northern Territory, where the population is showing a similar decline (Fukuda et al. 2015). Less is known about populations in Queensland, which may have been stable for the past decade. Harvesting of freshwater crocodiles is relatively minor, and the lack of economic value is reflected in the lower monitoring levels.
The dugong (Dugong dugon) is protected under the EPBC Act as a listed migratory and marine species. In Australia, dugongs occur in subtopical and tropical coastal and island waters from Shark Bay in Western Australia to Moreton Bay near Brisbane (Marsh et al. 2011). Small numbers of dugongs are found in New South Wales waters in summer, or when severe weather events strike southern Queensland (Allen et al. 2004).
Although dugongs are the most abundant marine mammal in the coastal waters of northern Australia (Marsh et al. 2011), their national status is unknown. Long-term monitoring has been limited throughout most of their range outside the east coast of Queensland and Torres Strait. Woinarksi et al. (2014) concluded that the status of dugongs in Australia is ‘near threatened’ using International Union for Conservation of Nature (IUCN) criteria. Based on several lines of evidence, Marsh et al. (2015) concluded that the Torres Strait subpopulation, the largest in the world, has been stable since the mid-1980s, despite significant levels of Indigenous harvest. However, concern exists about the status of the subpopulations along the east coast of Queensland, particularly in the southern Great Barrier Reef region south of Cooktown (Sobtzick et al. 2012), the region most affected by human development.
The main threats to dugong populations are gill-netting in Queensland, including in the Gulf of Carpentaria, and loss of seagrass habitat (see Seagrasses) to terrestrial run-off—the effect of which has been exacerbated by grazing, coastal development and extreme weather events, especially flooding and cyclones. A series of severe wet seasons culminating in the extreme weather events of the summer of 2010–11 had significant impacts on the dugong’s seagrass habits in Queensland, with consequent impacts on the region’s dugongs (Sobtzick et al. 2012, Meager & Limpus 2014, Fuentes et al. 2016). Vessel strikes are a localised threat to dugongs in populated areas. Native title holders are permitted to hunt dugongs in their sea Country. The local effects of such hunting are unknown outside Torres Strait, where the dugong subpopulation appears to be stable, as previously explained.
Most scientific data on the distribution and abundance of the dugong in Australia stem from aerial surveys, but the timeseries of information required for assessing trends does not exist outside the east coast of Queensland and Torres Strait. For much of the dugong’s range, the information is based on only 1 or 2 surveys, or is out of date or non-existent. Surveys have recently been conducted along the Onslow and Kimberley coasts in Western Australia, and in the Northern Territory. However, in the absence of adequate timeseries, it is impossible to confirm the dugong’s status in these areas.
Surveys have been limited by the availability of funding, compounded by complex logistics in remote regions, especially because of the need to limit surveys to restrictive weather conditions. Dugongs may be mistaken in aerial surveys for the co-occurring Australian snubfin dolphin (Orcaella heinsohni). Such misidentifications are most likely in the Northern Territory, as populations of snubfin dolphins are very small in most other parts of the dugong’s range. Telemetry studies have been used to understand dugong movements and habitat use, and to develop locally relevant correction factors for animals that are unavailable to observers during aerial surveys. In Moreton Bay, vessel-based mark–recapture studies have also been used with a view to providing information on population size, trends, health genetics and movements. This technique has the potential to produce more accurate population estimates than aerial surveys, but will be logistically difficult, if not impossible, to use in remote areas because of the challenge in meeting the assumptions of mark–recapture studies.
In Queensland, the timeseries of aerial surveys since the 1980s has detected a decline in dugongs for the northern Great Barrier Reef region (where it is not yet statistically significant; Sobtzick et al. 2014, 2015) and in the southern Great Barrier Reef region (Sobtzick et al. 2012, 2015). In addition, the size of the subpopulations along the urban coast of Queensland south from Cairns are considered substantially reduced relative to the 1960s (Marsh et al. 2005), because of a combination of netting, habitat decline, boat strike and Indigenous hunting.
Dugong subpopulations in Western Australia and the Northern Territory are less exposed to anthropogenic activity than on the urban coast of Queensland. Dugong abundance along the entire Northern Territory coastline was estimated for the first time in 2015 (Groom et al. 2017), with approximately 60 per cent of animals occurring in the Gulf of Carpentaria. The impact of fishing in the Northern Territory, particularly by gill-netting, is difficult to determine, and the status and extent of the seagrass beds are largely unknown.
In Western Australia, the largest and most secure subpopulation is in Shark Bay (Hodgson et al. 2008, Marsh et al. 2011). Other important dugong areas are in Exmouth Gulf (Hodgson et al. 2008), in the Onslow region (Department of Parks and Wildlife, Western Australia, pers. comm., 2016) and in the Kimberley (Bayliss et al. 2015).
Protecting the quality of the coastal environment (e.g. further reducing terrestrial run-off and industry pollution), in particular, seagrass communities, is crucial for ensuring the ongoing viability of the dugong in Australian waters. Dugongs have very slow reproductive cycles, such that even small reductions in survival are likely to have substantial impacts on population viability (Marsh et al. 2011). The National Dugong and Turtle Protection Plan 2014–17 has pledged $5.3 million to address the pressures on dugong and turtle populations, and may assist with recovery (DoE 2015).
The short-term and long-term outlook along the urban coast of Queensland is poor (i.e. this subpopulation will likely continue to deteriorate because of ongoing habitat loss unless terrestrial run-off is reduced). The outlook along the remainder of the dugong range is better in the short-term, but will likely deteriorate in the long term if there is further development in the remote north of Australia, or if seagrass meadows and dugong health are significantly affected by climate change.
Fishes in bays and estuaries
Many coastal fish species use bays and estuaries at the juvenile stage in their lifecycle (Potter et al. 2015). Most commercially important fish spawn in the coastal ocean and recruit to estuarine areas. Fish are an ecologically and economically important resource for commercial and recreational fishing. Most fish use rocky reef, seagrass and mangroves as nursery habitat (Blandon & Zu Ermgassen 2014). For example, juvenile King George whiting (Sillaginodes punctatus; Moran et al. 2004) recruit to seagrass beds, whereas juvenile pink snapper (Pagrus auratus) recruit to deep, sandy regions (Hamer & Jenkins 2004). Therefore, some of the main threats to fish populations occur when these habitats are degraded by coastal development, urban run-off, dredging, trawling and activities that increase sedimentation. Recent studies show that some estuarine species (estuary perch, yellowfin bream, sand whiting) show remarkable fidelity to small areas, leading to the potential for local depletion (Gannon et al. 2015). Other areas of coasts and estuaries appear to be recruitment hotspots, characterised by a persistent abundance of juvenile fish (Ford et al. 2010), because of habitat or favourable currents. Such areas should especially be targeted for protection or rehabilitation.
As adults, fish that began their life within estuaries may be targeted by commercial and recreational fishers within those same estuaries or when they migrate offshore. Most commercial fisheries across Australia are regulated and monitored in some form; however, a substantial number of fish species stocks remain unassessed (Beeton et al. 2012). Moreover, information on the status of recreational targeted fish populations is often absent unless the fish species is also a commercially targeted fish. Detailed data on estuary-dependent fish in New South Wales are generally limited to commercially or recreationally important species, such as yellowfin bream (Acanthopagrus australis), sea mullet (Mugil cephalus) and mulloway (Argyrosomus japonicus). Fisheries-sourced data suffer from gear, effort and species biases, and fisheries-independent data are required for meaningful assessments.
Reef Life Survey has conducted fish counts in several bays around Australia since 2005 (Edgar & Stuart-Smith 2014). Two of these bays show increasing numbers of reef fish, 1 shows decreasing numbers, and 2 show no significant change (Figure COA14). New tropical fish species are an increasing occurrence off Sydney (Figueira & Booth 2010), as they are off Tasmania (Last et al. 2011), such as a large coral trout Plectropomus sp. captured off Sydney in 2015 (Australian Museum records), and tropical surgeon fishes (Basford et al. 2016). Increases in fish numbers at some sites may be partly because of protection measures such as marine sanctuaries, but may also be related to increased temperatures favouring warm-water species (Vergés et al. 2014).
The primary issues of concern for fish populations in bays and estuaries vary among the states. Effects of warming coastal waters are particularly pronounced in New South Wales (Figueira & Booth 2010), where the southward spread of low-productivity tropical water combines with the pressures of urbanisation of Newcastle, Sydney and Wollongong. The strengthening East Australian Current has increased the temperature and salinity of coastal water, such that oceanographic conditions have shifted southwards by 350 kilometres (Ridgway 2007), and the ecological and economic impacts are just beginning to be realised around Australia (Johnson et al. 2011). Recreational fishing pressure in New South Wales is considered to be very high because of the high density of coastal population and the large number of residents with fishing licences; however, data on recreational fishing take are scarce (Beeton et al. 2012, Mayer-Pinto et al. 2015). Urbanisation also has the effect of greater chemical, light and noise pollution in the aquatic environment. Noise has recently been found to reduce foraging by mulloway (Payne et al. 2015a)—one of the main estuarine predators necessary for normal ecosystem function—and artificial light has been shown to increase fish predation on benthic invertebrates in Sydney Harbour (Bolton et al. 2017). Chemical pollution and habitat modification appeared to have substantial effects on larval fish in heavily modified estuaries of New South Wales (McKinley et al. 2011a), but effects on juvenile–adult communities surveyed by beach seine were not detectable (McKinley et al. 2011b).
Reduced freshwater flow is a key issue in southern Australia, affecting estuarine water quality, habitats and, consequently, fishes (Ferguson et al. 2013). Fisheries are also affected, such that drought-declared regions incur reduced catch per unit effort of 4 species across 7 New South Wales estuaries (Gillson 2011). Estuarine fisheries could qualify for drought relief support. Reduced freshwater flow increases marine influence, and pushes the salt wedge further inland, where it may miss areas of critical benthic habitat. Therefore, freshwater flow is important for normal functioning of estuaries and justifies the importance of environmental freshwater flows (e.g. for fish behaviour; Payne et al. 2015b). In the Peel–Harvey Estuary of Western Australia, salinity has risen because of a combination of climate-induced flow reduction and construction of an artificial channel to the sea, and this has increased the proportion of opportunistic marine fish in the estuary (Potter et al. 2016). The Peel–Harvey Estuary was artificially opened in response to eutrophication, which still plagues other estuaries and their fish populations in Western Australia (e.g. Hallett et al. 2016c). Some New South Wales estuaries are managed by increased opening frequency, but, therefore, may incur greater sand build-up and colonisation by mangroves.
In the south-west, species diversity is greater in permanently open estuaries (Valesini et al. 2013). Fishes are negatively affected by hypersalinity, habitat loss, and greater frequency and longevity of hypoxic events. Reduced freshwater flows, rising sea levels and increased storm surges may increase the period for which ICOLLs are closed by sandbars, affecting the lifecycles of marine species and diadromous fish (species that migrate between marine and freshwater habitats, usually as part of their reproductive cycle) (Gillanders et al. 2011).