Coastal river and estuary pollution

Pollution is a longstanding pressure on coastal rivers and estuaries, particularly in areas of urbanisation, industrialisation, mining and agriculture. There remains a legacy of pollution associated with early European history in Australia (Wolanski 2014), and both legacy chemical contamination and contemporary inputs to poorly flushed systems are among the most significant pressures on coastal waterways. Common contaminants found in coastal rivers and estuaries include excess metals, nutrients and organic matter (see Nutrient pollution), and industrial chemicals, pesticides, herbicides, terrigenous sediments and debris (see Marine debris).

Ecological consequences of pollution in coastal rivers and estuaries include loss or change of biodiversity, habitat, ecosystem function and ecological processes (Johnston & Roberts 2009, Johnston et al. 2015). Bioaccumulation of toxicants in the food chain can also affect vertebrate population viability and human health (Hamilton et al. 2016). Most pollution results from historical legacies, ongoing diffuse sources (e.g. agricultural run-off and storm water) and waste management. There is a need for greater understanding of the bioavailability and toxicity of toxicants in both sediments and the water column, and for the development of sensitive biomonitoring tools such as those achieved for estuaries in south-eastern Australia (Edge et al. 2014).

New classes of contaminants such as plastics, cosmetic products and therapeutics are growing concerns (Galloway & Lewis 2016). There is little knowledge about the chemical compounds that many of these emerging contaminants degrade into once in sea water or sediment, and we do not know the full suite of their potential impacts. Detecting new contaminants and forming national-scale assessments are hindered by lack of national-scale data agencies, standardised monitoring programs, and the communication and accessibility of data.

Nationally, pollution pressure on many estuaries is moderate to strong, but both pollution levels and data availability vary greatly among locations. Existing data for most jurisdictions focus on modified estuaries, leaving knowledge gaps regarding effects of pollution in relatively unmodified estuaries (Hallett et al. 2016b, 2016d). In New South Wales, the condition of heavily developed coastal waterways is poor, and nutrients, metals, pesticides and other contaminants are found at high levels in some estuaries (e.g. Sydney Harbour, Port Kembla Harbour; Dafforn et al. 2012). Metal enrichment of sediments was found to be related to population density across 38 central New South Wales rivers and estuaries (Birch et al. 2015a). Between 1999 and 2010, sediment metal concentrations in Sydney Harbour declined in large sections of the upper and central estuary, but slightly increased in the lower estuary following urban and industrial shifts (Birch et al. 2013). Pesticide distributions in Sydney Harbour are linked to stormwater inputs (Birch et al. 2015b).

For estuaries in Queensland and northern New South Wales, major pollution sources are a combination of agriculture, mining, industry and urban land use. Several Queensland and New South Wales rivers and estuaries are moderately to strongly affected by sediments and pesticides. Agriculturally modified estuaries continue to suffer water quality issues, including major fish die-offs because of organic enrichment (see Nutrient pollution), and drainage of floodplains to cause acid sulfate soil run-off. Report card systems are in place for south-east Queensland, Gladstone Harbour, the Great Barrier Reef and Mackay, but monitoring has revealed little improvement in water quality during the past 5 years because of the scale of the problem and the cost of agricultural reform (GBRMPA 2014).

Pesticide contamination in the Great Barrier Reef catchment is widespread, and concentrations of the herbicide diuron exceed guideline trigger values at multiple sites (Smith et al. 2012). Diuron is used in the Queensland sugar cane industry and interferes with the photosynthetic activity of a wide range of organisms (Duke et al. 2005). Current understanding of nontarget effects of toxins is limited, and there is a need for greater knowledge of the risks of toxins in coastal areas to inform guidelines and management. Ideally, management should target the source of inputs, such as the Queensland bylaw that limits the use of diuron by the sugar cane industry.

Pollution in southern states receives less attention than issues related to flow regulation, but it is still a major problem in some areas. A high proportion of South Australian estuaries are in poor condition, and pollution as a legacy of industrial activity, land clearing and mining is common in Tasmania. In Victoria, pollution is not part of the Index of Estuarine Condition program (DEPI 2013), despite being a significant pressure in some estuaries. There are large and obvious impacts of pollution in the southern half of Western Australia, particularly in the south-west (Brearley 2005, Ward et al. 2010).

Much of far northern Australia is relatively unaffected by pollution because development pressure is low. Most of the Northern Territory coastline is unmodified and largely free from contaminants, although Darwin Harbour is an exception (DLRM 2013, 2014). Water quality in Darwin Harbour and its tributaries is generally good, but increased sedimentation and nutrients arise from dredging, sewage discharge, and wet-season stormwater flows (DLRM 2014), and herbicides and metals have been detected at low concentrations (French et al. 2015). In the dry season, the potential for poor water quality increases with water residence time (the length of time a parcel of water resides in a particular area) (Fortune 2010). The Northern Australia Development initiative will present various challenges in the form of pollutants from agricultural and extractive industries.

Improvements have been made in managing point-source pollutants, but diffuse pollutant sources (e.g. agriculture and storm water) make it difficult to reduce pressure in the presence of a growing population and catchment development. Remediation of contaminated sediments is expensive, so is usually only attempted for high-priority issues, such as the removal of dioxins from sediments in Homebush Bay, New South Wales. Management improvements exist or are planned in some states and regions, but lack of research funding and monitoring limits our understanding of their effectiveness. Legacy effects may continue for decades after management begins, which is detrimental to the public and political will required to sustain efforts. Australia has no national program of measurement or monitoring of contaminants in aquatic or terrestrial environments; however, the National Pollution Inventory does consolidate the reporting of emissions of 93 toxic substances from medium and large industries.

The input and environmental impact of pollutants are expected to rise with increasing catchment modification to support growing populations. Pollution is also likely to increase with land reclamation, dredging, waste disposal, agriculture and storm water (including floods and high flows), all of which increase with coastal population and development. Water quality could be improved by better water and sediment quality guidelines, monitoring, risk assessment tools, analytical techniques and measures to address the shortage of management action.

Nutrient pollution

Nutrients such as nitrogen and phosphorus are necessary for ecological functioning in coastal waters (Howarth & Marino 2006). They are required by algae for photosynthesis at the bottom of food webs, are transferred up the food chain by higher-order consumers, and are eventually recycled by detritivores (animals that eat detritus including decaying plant and animal remains) (Moore et al. 2013). The definition of excess nutrients can be ecosystem dependent, rather than based on universal loads or concentrations, since ecosystems vary in their requirements and cycling rates. Excess nutrients can have severe negative environmental consequences (Chislock et al. 2013) and lead to:

• eutrophication (where excess nutrients encourage algal growth)
• harmful algal blooms (see Algal blooms)
• high turbidity (see Water turbidity, transparency and colour)
• creation of coastal low-oxygen dead zones (see Coastal low-oxygen dead zones)
• disruption of natural biogeochemical cycling (see Microbial processes and nutrient cycling)
• crown-of-thorns outbreaks, coral bleaching and coral disease in tropical areas.

Nutrients enter coastal waters through 2 main pathways: point-source effluent such as sewage outfalls, and diffuse sources such as agricultural run-off. Practices that contribute to diffuse nutrient pollution include clearing of native vegetative (which decreases sediment stability), the creation of impervious surfaces in urban areas (which increases the quantity and water velocity of run-off) and the use of bulk quantities of nutrients in the form of fertiliser in the agricultural industry. These practices have facilitated large quantities of nutrients entering coastal waters, particularly during large flood events.

Intensive agriculture in the Great Barrier Reef catchment has resulted in substantial nutrient input into the naturally oligotrophic (low primary productivity) coastal waters (Kroon et al. 2016). Since 2003, the Australian and Queensland governments have implemented a range of policy initiatives to reduce land-based pollution of the Great Barrier Reef. The most significant of these is the Reef Plan, which includes projects to monitor, model and experiment with management options for pollution sources and pathways in farms and catchments. In particular, the Great Barrier Reef Catchment Loads Monitoring Program measures water quality entering the Great Barrier Reef lagoon from priority catchments, and estimated that 12,000 tonnes of nitrogen and 2900 tonnes of phosphorus came from monitored catchments in 2014–15 (Wallace et al. 2016). Despite management efforts, however, total nitrogen entering the Great Barrier Reef continues to increase, and it is doubtful that current management actions are sufficient to reach Reef Plan targets (Kroon et al. 2016).

In New South Wales, temporal trends in chlorophyll-a, an indicator of total nitrogen, are being researched (Roper et al. 2011). Satellites provide a means of measuring surface chlorophyll-a across extensive areas, but data are at the 1 × 1 kilometre scale and are patchy because of cloud cover, so often have high uncertainty. In the short term, nutrient monitoring will depend on in situ measurements, whereas, in the long term, more accurate methods should be developed to measure phytoplankton biomass and primary productivity. Efforts may be best focused on improving methods for detecting and avoiding the release of excess nutrients.

Marine debris

Coastal marine debris is a term for human litter in the coastal zone. Most debris enters the water in urban areas, but is often transported to remote locations by wind and currents (Reisser et al. 2013, Critchell et al. 2015). The majority (82 per cent) of impacts from debris are attributed to plastics (Rochman et al. 2015), and approximately three-quarters of the debris found along the Australian coast by a recent CSIRO survey was plastic. The Australian plastic industry produces about 1.2 million tonnes of plastic each year, some of which ends up in waterways and does not biodegrade. It does, however, photodegrade under sunlight, and some animals can break the material into small pieces (Davidson 2012).

In 2009, a national threat abatement plan was implemented to address marine debris impacts on marine vertebrates. Debris can entangle marine animals, such as in the Gulf of Carpentaria where an estimated 5000–15,000 turtles become ensnared in discarded fishing nets (Wilcox et al. 2015). Debris can also be ingested by shorebirds (Verlis et al. 2013, Lavers et al. 2014), turtles (Koelmans 2015) and invertebrates (Canesi & Corsi 2016), and accumulate inside individual animals (Browne et al. 2008).

Policy-makers are requesting that populations (and assemblages), rather than just individual organisms, should be protected from debris (SECRC 2015). Population models provide a means to assess whether a population is declining; the cause of decline, if occurring; the parts of the lifecycle requiring managerial action; and the likely fate of the population. Where these models are not possible, alternative models can be used as a precautionary measure to manage mortality or serious injury of some threatened and endangered vertebrates caused by debris, using the concept of ‘potential biological removal’ (Browne et al. 2015). Models are also being developed to synthesise pathological data that might link debris to mortality (Baulch & Perry 2014). Regardless of such problems, using these approaches to estimate the likelihood and potential magnitudes of impacts of debris is a useful precautionary action until better information is available.

Of emerging concern are microplastics, which are small particles that are micrometres in size (Browne 2015). These enter coastal waters through sewage contaminated by fibres from washing clothes or from cleaning products; they can also occur from the fragmentation of larger plastics. The ecological effects of microplastics are largely unknown (Vegter et al. 2014), but pathways of impact include blockage of digestive tracts and the transfer of organic toxins through food webs (Browne et al. 2013, Rochman et al. 2013). Research about the impacts of microplastics is growing, although variation in particle size among studies limits the ability to determine generalities.

Little scientific evidence exists to assess the pressure of coastal marine debris in Australia. Most studies focus on distribution or exposure, and do not consider impacts or risk to the environment (Rochman et al. 2015), and there remains a skewed proportion of studies on sandy beach habitats. Inconsistency in methodology, definitions of marine debris and the scale of studies hinders identification of general patterns in marine debris globally (Browne et al. 2015). In recent years, research has increased at the local and national levels, with a focus on determining baseline conditions.

Public awareness and concern regarding coastal debris are high. Various clean-up initiatives, such as Clean Up Australia, Keep Australia Beautiful and the Tangaroa Blue Foundation (see Box COA4), have gathered data on coastal debris. South Australia’s aquaculture industries launched their ‘Adopt a Beach’ program in 2012, whereby aquaculture companies agree to regularly collect marine debris and accompanying data from ‘adopted’ beaches. However, well-designed scientific and analytical studies conducted on appropriate spatial and temporal scales are still necessary to determine quantities, accumulation rates, patterns, pathways and sources of debris nationally. This exposure information should then be linked to social, economic and ecological impacts through time (e.g. Pearson et al. 2014).

There is a need to minimise input and improve management practices from sources (urban and agricultural areas) to sinks (waterways and coastal zones). Possible actions include container deposit schemes, plastic bag bans and microbead bans, but microplastics remain a key challenge. There is a need to address human attitudes and behaviour towards product use and littering, and a greater emphasis on designing products that produce less waste (Eagle et al. 2016).

In the short term, debris is expected to increase because managerial responses have been slow to emerge. Managerial activities should reduce inputs in the long term; however, legacy debris will continue to impact the ecosystem. An important issue is whether the impacts of marine debris should be managed under existing legislation and policies, or whether they warrant separate attention.

Rising sea temperatures

Since the beginning of the 20th century, the average temperature of Australia’s coastal waters has risen by 0.9 °C (BoM & CSIRO 2014). Rising sea temperatures are associated with shifts in species distributions, coral bleaching, increased risk of harmful algal blooms (see Algal blooms), and impacts on fishing and aquaculture (Welch et al. 2014). Increasing climatic variability, observable as extreme events such as marine heatwaves, may be as important as change in average temperature. Marine heatwaves are increasing in intensity, duration and frequency, with potentially dire consequences for organisms already stressed by higher average temperatures.

Sea temperature affects both growth and reproduction of marine organisms. Species can respond to rising temperatures in 3 main ways: by shifting in range, changing the timing of life history events or changing in physiology (Bellard et al. 2012). Rising sea temperatures are extending the range of populations southwards (Vergés et al. 2014), and gradually resulting in the tropicalisation of temperate ecosystems. Tropical fish are now commonly found in Sydney Harbour during late summer, and have even been found surviving winter (Figueira & Booth 2010).

In Western Australia, the impact of temperature change is most concerning in the mid-latitudes between Ningaloo and Jurien. The La Niña of 2011 resulted in a marine heatwave off the Western Australian coast, which led to widespread impacts, including the decimation of kelp forests (Wernberg et al. 2013). This event caused profound changes in marine ecosystems that have yet to be reversed, including coral bleaching, fish and invertebrate deaths, and changes to species distributions and community structure. South-western Australia has lower seasonal variability and evolutionary stability than tropical areas, making it more sensitive to change. Differences in the sensitivity of ecological communities to temperature change limit the potential to generalise assessments across the east and west coasts of Australia.

On a national scale, sea temperature is predicted to continue to rise, together with the frequency of marine heatwaves. In the short term, El Niño may reduce sea temperature increases for the south-west of Australia, whereas the south-east will experience higher mean temperatures (Oliver & Holbrook 2014), more extreme temperatures (Oliver et al. 2014), and larger and more persistent warm core eddies (Oliver et al. 2015). Such patterns were observed in 2016 and caused a mass coral bleaching event on the Great Barrier Reef (see the Marine environment report for details). The frequency and intensity of ENSO cycling may double. In the short term, species and habitats will continue to shift southwards and along estuaries. Rising sea temperatures may eventually contribute to the loss of species, assemblages and entire habitats, although some species are expected to benefit from warming conditions.

Separating anthropogenic temperature change from natural climate cycles such as the Interdecadal Pacific Oscillation and the Southern Oscillation is difficult, and adds uncertainty to future sea temperature projections. Better identification of thresholds at which organism level changes result in the loss of species is also important to understand how community structure will change with future sea temperature increases.

Flow regimes

Freshwater inflow delivers nutrients and sediments (see Sediment transport), maintains salinity regimes of rivers and estuaries, and feeds local groundwater sinks. Several habitats and species (e.g. shorebirds, fish, invertebrates) depend on freshwater flows and the functional processes that these flows perform. Fresh water is also a valued resource for human activities, required for irrigation, industry, drinking water and the environment.

Flow regimes are susceptible to impacts from climate change (Teng et al. 2012), population growth and coastal development. Structures that regulate flow (e.g. weirs and dams) have altered natural flow volumes; and flood frequency, duration and variability; and have contributed to the loss of biological diversity and ecological function in aquatic ecosystems (CSIRO 2011).

Flow regimes in the south and east of Australia are dramatically altered from their natural state, largely because of diverting of water for irrigation and regulation (CSIRO 2008). Ongoing low flow to the Murray River, particularly during the millennium drought (which occurred from 2000 to 2010—although in some areas it began as early as 1997 and ended as late as 2012; Chiew et al. 2014), is affecting the Lower Lakes and Coorong Ramsar wetland (MDFRC 2014), and has been the subject of intense political debate for many years. Of note is the associated degradation of a key migratory bird food resource, widgeonweed (Ruppia spp.), and the continuing hypersalinity of the South Lagoon in the Coorong (Paton & Bailey 2012).

The coastal freshwater lens aquifers on the Eyre Peninsula, where unconfined aquifers are hydraulically connected to the ocean, are also exploited to maximum capacity. It is unknown whether local ecosystems are dependent on this discharge and, if so, whether they are affected by groundwater extraction reducing discharge. Groundwater extraction may also cause seawater intrusion, and the contamination of aquifers used for irrigation and public use (see Seawater intrusion), although current monitoring shows no evidence of increased groundwater salinity in these locations.

Despite groundwater monitoring being difficult and expensive, South Australia has implemented a network of observation sites that have lowered the risk of significant reductions in coastal discharge. Implementing similar networks in other at-risk areas is important to minimise future changes to natural flow regimes across Australia. Alternatively, the purchase of environmental flows to return waterways to more natural flow regimes can improve conditions.

Long-term monitoring of streamflow and water quality at more locations is necessary to provide important baseline information to assess trends and to establish links between processes. More advanced modelling that integrates data on climate, hydrology, water quality and environmental impacts would increase the accuracy of future predictions.

Seawater intrusion

Groundwater is an important water source for sections of Australia’s growing coastal population, but it is under pressure from seawater intrusion, which increases the salinity of freshwater aquifers. Key causes of seawater intrusion are unsustainable groundwater extraction, rising sea levels, variable precipitation regimes, coastal development and land-use change. Groundwater extraction increases with drying conditions (e.g. as has occurred in south-western Australia), population growth and industrialisation (Wada et al. 2010). Groundwater extraction pressure is strongest around large population centres, such as Perth and Adelaide.

Because of the difficulty and cost of monitoring, empirical data on groundwater extraction rates, volumes and salinity are often not available. Consequently, very little is known about the impacts of seawater intrusion beyond theoretical predictions of increased groundwater and soil salinity. The degree of research and knowledge among jurisdictions is linked to the relative economic value of groundwater. Groundwater reserves can support diverse and valuable ecosystems (Goonan et al. 2015) depending on land use (Korbel et al. 2013), but consideration of ecological impacts of seawater intrusion is usually secondary to human water needs.

In a national assessment of coastal aquifers with data to estimate vulnerability to seawater intrusion (i.e. hydrologic, hydrogeologic and physiographic data), 47 per cent had high vulnerability—a value predicted to increase to 57 per cent in the future (Ivkovic et al. 2012). There are signs of current or potential seawater intrusion in all states, except Tasmania, where data are lacking. New South Wales, Victoria and Tasmania are less dependent on groundwater than other states, and the risk of seawater intrusion is therefore of less concern. However, these states still have some potential hotspots (Ivkovic et al. 2012). In Queensland, Western Australia and South Australia, seawater intrusion risk is high and has been observed in several locations (Ivkovic et al. 2012). Extensive areas of low-lying coast in the Northern Territory are vulnerable to intrusion because of sea level rise and inundation (see Box COA5), although data are lacking in the Northern Territory to make adequate assessments.

Many aquifers around Australia are managed, but groundwater management tends to only use freshwater models and ignore seawater intrusion. In the short term, poor management is expected to continue unless decisions are informed by appropriate monitoring and research. The National Coastal Groundwater Management Knowledge Transfer Workshop 2013 identified a need for national guidelines, ongoing monitoring, increased research and the retention of information (Cook et al. 2014). In 2013, the Australian Government released guidelines for groundwater quality protection in Australia. In the longer term, climate change is expected to reduce regeneration rates of groundwater supplies, particularly in the south-west, while sea level rise should increase salinisation rates in low-lying regions. The permanent salinisation of groundwater resources may force the exploration and exploitation of new aquifers.

Water abstraction

Fresh water is removed (or ‘abstracted’) from waterways for many purposes, including irrigation, industrial applications and public use. In many cases, abstraction occurring upstream has profound ecological impacts in coastal regions downstream, including eutrophication, hypersalinity, algal blooms and reduced productivity in estuaries. Altering freshwater input to coastal waters can cause saline waters to move upstream into previously fresh areas, affecting biological diversity and productivity.

The degree of water abstraction is linked to development intensity, being greatest in the south-east and south-west of Australia. Cooperative efforts across some states (e.g. New South Wales, Victoria and Queensland) to better manage water abstraction and environmental flows may act to mitigate impacts, and to stabilise environmental impacts in the short term. Some rivers, such as in parts of northern Australia that are less developed, are not yet affected by water abstraction. Data on water abstraction are poor, particularly for small dams in farms, limiting the ability to make Australia-wide assessments.

Most rivers in New South Wales, Victoria and south-east Queensland, and some in south-west Western Australia, experience upstream abstraction, although it is generally low in the north of each state. No major dams have been recently built in New South Wales, Victoria or Queensland, although there have potentially been some recent increases in abstraction for irrigation or construction of small dams. The Murray River is the main river feeding the coast in South Australia and  has experienced substantial abstraction; however, in the past 5 years, greater flooding and environmental flows have improved the condition in the lower Murray–Darling Basin. Although many Tasmanian rivers are dammed, water abstraction there is low; however, it has been increasing in recent years. Similarly, in the past 5 years, there has been a small increase in abstraction in the Northern Territory, where abstraction pressure has historically been low.

The outlook for water abstraction as a pressure is stable in the short term, barring small increases predicted in Tasmania. The long-term outlook is for increasing abstraction as development and the accompanying need for water increase in northern Australia. Demand for water will only increase in the future as coastal populations rise (Wolanski 2014), necessitating more infrastructure to remove water otherwise intended for downstream coastal ecosystems. A major option for reducing this pressure in line with global trends is the increasing use of recycled water, including for drinking water, as suggested by recent studies (Khan 2013).

Dredging

Dredging is the practice of removing and relocating sediment from the seabed, and is used to increase water depth for vessel movements, maintain flushing of estuaries, extract construction materials (e.g. sand for concrete or land reclamation) and supplement locations with a negative sediment budget. In Australia, nearshore dredging is most often associated with port maintenance and development, and clean dredged sediment is dumped to another area of seabed if not needed.

Dredging removes soft-sediment habitat and causes sediment resuspension, which increases turbidity. If sediments are contaminated, disturbing them by dredging can cause toxicants to be released into the water column (see Water turbidity, transparency and colour), where they can cause ecological impacts (Knott et al. 2009) and become bioavailable and spread beyond the immediate dredging zone (Hedge et al. 2009). Taxa directly or indirectly affected by dredging include seagrasses, seaweeds, corals, fish, epifauna (animals living on the surface of the seabed or riverbed) and infauna (animals living within ocean or river sediment). Deposition of dredge spoil also requires careful management to avoid the creation of large plumes.

The Environment Protection (Sea Dumping) Act 1981 regulates the disposal of waste in the marine environment, and works in conjunction with the Environment Protection and Biodiversity Conservation Act 1999 (EPBC Act) on impacts of national environmental significance. In 2015, a new regulation under the Great Barrier Reef Marine Park Regulations 1983 came into effect, prohibiting the dumping of spoil from capital dredging (removal of large amounts of material for the passage of shipping) projects in the Great Barrier Reef Marine Park. This prohibition was broadened to encompass the Great Barrier Reef World Heritage Area (GBRWHA) by the Queensland Sustainable Ports Development Act 2015, which prohibits the construction of new ports or expansion of existing ports outside identified priority ports, and prevents disposal of capital dredge in the GBRWHA. This regulation does not cover the disposal of maintenance dredging material, which may be produced frequently and in substantial quantities (McCook et al. 2014).

Impacts of dredging are usually restricted to within a few kilometres of dredge and dumping sites, but range in severity from moderate to high. However, this depends on the size of the activity and specifics of the deposition location, and considerable uncertainty often surrounds likely impacts of proposed dredging (Fisher et al. 2015). Furthermore, dredging impacts need to be considered in the context of background suspended sediment and ‘natural’ sediment dynamics, such as those associated with storms and river run-off. The temporal window of impacts usually ranges from weeks to months, but longer-term issues of legacy, chronic and cumulative impacts arise if dredging is frequent or disposal sites are not suitable. Dumping of contaminated sediments is now banned, and contaminated sediments must be disposed of as toxic waste, which has dramatically reduced toxic impacts from dredging beyond the initial suspension of sediments.

Maintenance dredging in New South Wales is common, and, although potential impacts are considered as part of the development approval process, they are rarely quantified. Release of contaminants from resuspended sediments is possible where port expansions are occurring and bedded sediments include a substantial legacy of contaminants, as is the case for most existing ports (Knott et al. 2009). In Port Phillip Bay in Victoria, dredging has occurred in uncontaminated and contaminated sediments over short spatiotemporal scales, in some cases potentially releasing contaminants into the water column.

Capital dredging in tropical Australia in the past 5 years has largely been related to the resource boom and the accommodation of large vessels (Ports Australia 2014a). Much dredging activity has recently occurred in Queensland ports, with extensive environmental assessment required before permission is granted. In general, monitoring of impacts of Queensland dredging activities on corals and seagrasses has been adequate, although concerns remain about instances where best practice has not been implemented, and/or there are potential indirect impacts such as disease. Similarly, many large dredging projects have been undertaken in Western Australia, many of which received considerable monitoring and had tightly regulated impacts (Hanley 2011). Although the number of dredging proposals and approvals has increased in Queensland and Western Australia, so too has awareness of and and adherence to environmental regulations.

Detailed information on dredging volumes, deposition sites and potential impacts is required before commencing dredging operations. However, in many cases, not all alternatives to dredging (e.g. longer jetties) are fully explored. Additionally, following approval, environmental impact monitoring is not always conducted, or is restricted to physicochemical data only. Consistent and interpretable up-to-date data on environmental impact and sediment dynamics collected at all stages of the dredging process would help facilitate decision-making, and ultimately reduce environmental impacts. Policies are needed to encourage learning, objective assessment of short-term and long-term spatial impacts, and the application of this information.

Assessing future impacts of dredging is a difficult task without specific information on areas where dredging is likely or planned in the future. The outlook for dredging in the short term is stable but potentially increasing, because most work is currently maintenance. However, this may change if climate-related coastal impacts require an increased dredging response, including more frequent beach nourishment from offshore sands. Maintenance dredging will always be required and is expected to increase with the predicted increases in shipping activity. Capital dredging will be needed for new ports, developing existing routes and accommodating larger vessels. Continued research into the impacts of dredging, and improved management and regulation should help reduce long-term effects, although increasing developments in relatively pristine regions, if poorly planned or managed, may have unacceptable detrimental effects.

Fishing

Australia has a long history of fishing, extending back to traditional practices of Indigenous communities. Some traditional fishing practices continue, and represent an important component of Indigenous culture (Feary 2015; see Box COA6). This report covers fishing practices specifically associated with the coast, such as shore-based line fishing, and fishing within bays and estuaries. Fishing is now one of Australia’s most popular recreational activities and is argued to be a lucrative enterprise, with an estimated value nationwide of $1.85 billion in 2000–01 (Henry & Lyle 2003, Campbell & Murphy 2005), although contention remains around how to accurately calculate the economic value of this activity (Figure COA9; Table COA1). Fishing pressure is concentrated around population hotspots and centres of commercial operations, with remote coastal waters generally under lower fishing pressure.

Pressures from fishing can include:

• overharvesting (including for bait collection)
• associated impacts from off-road vehicles and foot-traffic disturbance of vegetation
• litter
• disruption of food webs
• alteration of species and genetic compositions
• habitat destruction
• entanglement with fishing gear.

The removal of top-order predators through overharvesting can have cascading effects on the structure of food webs, particularly through selective fishing of key species (Bascompte et al. 2005). Impacts of fishing depend on factors such as the method of capture, residency and life history of the species. Public understanding of the consequences of fishing pressure in Australia is increasing as no-take marine park zones are established around the coast.

The amount of shore-based fishing or fishing from boats in estuaries is believed to be declining or stable in most states during the past 5 years, although it is difficult to quantify since it is often unmonitored. State and territory governments are responsible for managing recreational fishing in their jurisdictions, and some, such as the Victorian Government, are actively trying to increase recreational fishing. In Queensland, the Northern Territory, Tasmania and South Australia, recreational fishing pressure is high near boat ramps and accessible locations near population centres, but is much lower in remote areas (e.g. Gulf of Carpentaria, western Tasmania, west coast of South Australia).

Coastal commercial fishing is patchy, being concentrated near productive sites or near ports. The trend during the past 5 years varies between fisheries. Abalone fisheries are declining because of disease and legacy overfishing, whereas snapper catch (recreational and commercial) in Port Phillip Bay has increased during the past 20 years. The decline in some commercial fisheries is partly attributed to tightening regulatory controls, including restrictions on the number of entrants, total effort and/or total catch, and the activities and methods allowed. Commercial netting is planned to be phased out of Port Phillip Bay by 2022, and other areas may follow suit.

Interaction between recreational and commercial fisheries is an issue of concern, and both stakeholders have concerns about the activities of the other. This is partly because of limitations in recreational fishing data, because monitoring is scarce for certain types of fishing (e.g. shore based) and data quality varies between states. For example, no shore-based recreational licence is required in Western Australia or Tasmania, making it difficult to quantify the number of fishers. Monitoring is often dispersed and ad hoc, particularly in remote areas. Developments in aerial surveys may alleviate this data gap, as indicated by recent studies of recreational fishing in remote Western Australia (Smallwood & Beckley 2012).

In the short term, recreational fishing pressure may rise as coastal populations grow and new technologies for finding fish become widely available. Some such increases may be offset by improvements in stock sustainability, recovery programs, ecosystem management and public awareness. In the long term, uncertainties exist about the impacts of multiple pressures, such as climate change and technological progress, and there are increasingly divided views on what are acceptable impacts from fishing.

Table COA1 Participation statistics from the National Recreational and Indigenous Fishing Survey and statewide surveys, 2000, 2007, 2010 and 2012–13

Note: Participation and fishing days data for South Australia (SA), Tasmania (Tas) and Queensland (Qld) are only for residents of each state. Northern Territory (NT) data are for all residents surveyed in 2000, but 2010 data exclude Aboriginal and Torres Strait Islander people.

Sources: Savage & Hobsbawn (2009), Fisheries Research and Development Corporation

Artificial reefs

Artificial reefs include materials of opportunity (scuttled ships, rubble piles) as well as designed underwater structures providing complex hard-surface habitat for fish and benthic invertebrates. Installing artificial reefs often aims to increase biomass of fish targeted by anglers, with the added potential to increase productivity of other fishes or trophic levels. Artificial reefs can also be deployed for recreational purposes such as diving or surfing, or for shoreline protection. Although artificial reefs often have high social value, the ecological benefit of localised increases in fish biomass is debated, and they can also cause localised impacts on nontarget communities (Bohnsack 1989, Koeck et al. 2014, Smith et al. 2015). Artificial reefs alter the sea floor, typically changing it from sand to hard substrate, but also cause shading and create a ‘halo’ effect of increased scouring, predation and organic matter deposition in an area of soft sediment that extends beyond the physical constraints of the reef (Dafforn et al. 2015). Note that this assessment differs from that of the Marine environment report, which focuses only on the effects of artificial reefs on fish.

Recent research has aimed to assess impacts of artificial reefs on various components of the ecosystem (Jebreen et al. 2003), but there is lack of agreement on what constitutes a positive or negative change (e.g. increased productivity) and the appropriate metrics to quantify these effects (Claisse et al. 2014; Smith et al. 2015, 2016). Many studies of artificial reefs are fish orientated, and the varied design, construction and monitoring of artificial reefs limit understanding of impacts (Ushiama et al. 2016). Artificial reefs can be exposed to considerable fishing pressure (Keller et al. 2016), but it is uncertain whether this leads to increased harvest rates.

In the short term, more reefs are planned for deployment, but it is unknown whether these will reach numbers that have more than localised impacts. It is possible that designed reefs on the open coast are not merely a fish attraction device, but facilitate a productive food chain from zooplankton to forage fish and reef invertebrates (Champion et al. 2015, Smith et al. 2016). In the long term, artificial reefs are set to become a more widespread feature of coastal waters as they become increasingly popular with key stakeholders, particularly recreational anglers.

Aquaculture

As of 2013–14, the aquaculture industry employd approximately 5000 people and had an estimated value of $994 million, an increase of $41 million since 2004 (Savage & Hobsbawn 2015). Tasmania and South Australia accounted for most of the aquaculture production (74 per cent) in 2013–14 (Savage & Hobsbawn 2015). Aquaculture production value and volume decreased from 2012–13 to 2013–14 (Savage & Hobsbawn 2015), although it is uncertain whether the cause was environmental or market related. The Australian aquaculture industry is currently small and relies on high-value products rather than bulk-production volumes.

Environmental impacts from aquaculture can be severe, but are usually local in extent. Large-scale impacts are rare, except where they result in the introduction and spread of disease or introduced species. Nutrient addition to coastal waters as part of finfish and prawn farming has high potential for environmental impacts and, accordingly, is highly regulated to minimise risk. For example, impacts below or adjacent to fish pens are managed by regular movement of the pens and feed control, so impacts of pens are usually contained. Pressures related to aquaculture vary between states; however, the impacts of feral Pacific oysters (Crassostrea gigas) are a significant concern for several states (Scanes et al. 2016).

In both New South Wales and Tasmania, the Pacific oyster industry has been severely affected by Pacific oyster mortality syndrome (POMS). Abalone is the main aquaculture product of Victoria, and both cultured and wild populations are affected by exotic disease and associated issues (Gorfine et al. 2008). In Queensland, all aquaculture is land based, with farmed prawns the major product. This is a relatively stable industry, but also vulnerable to disease and other environmental pressures. In Western Australia, pearl oysters are the major aquaculture sector, and are potentially susceptible to stress related to resource-extraction industries and climate change. The Northern Territory aquaculture industry is small and predominantly consists of land-based barramundi farming, although there are plans to develop and expand aquaculture in the north. In South Australia, tuna is ranched in coastal pens, creating some localised pressures on the coast. Tasmanian salmon farming in the D’Entrecasteaux Channel and Huon River has minor impacts on water quality (Ross & Macleod 2013). This industry is also challenged by rising water temperatures associated with climate change.

Research is needed into several topics, including patterns in, and causes of, mass mortality events, the dynamics of introduced diseases, interactions between these factors and environmental conditions, effects of aquaculture on ecosystems, and the effects of climate change on production and management. Harmful algal blooms threaten aquaculture operations and are discussed in more detail under Algal blooms. Another issue is appropriate biosecurity to deal with introduced species, and management of introduced species and disease transfer between aquaculture and wild populations. Addressing these questions should help inform best-practice management actions.

Rising demand for aquaculture indicates that environmental pressures resulting from the industry are likely to increase, with projections of stable growth in the short term accompanied by the development of new industries in seaweed production. In the long term, climate change will have a negative impact on many aquaculture species, particularly through ocean acidification, rising sea temperatures, altered precipitation regimes, inundation and extreme weather events.

Vessel activity and infrastructure

Vessels operate in Australia’s coastal waters for a range of purposes, including recreational boating, commercial shipping, transport and cruise shipping. Onshore infrastructure, such as moorings, marinas, boat ramps, sheds and large-scale ports, are required to store vessels and support operations. The distribution of vessel activity and associated infrastructure is patchy along the Australian coast, but this activity imposes considerable environmental impacts in heavily used ports and harbours.

The intensity of commercial vessel activity has increased since 2011, with many ports being expanded or built to accommodate the increase. In 2013–14, the busiest port in terms of total throughput was Port Hedland (Western Australia), which moved 373 million tonnes, most of which was bulk commodity exports (Ports Australia 2014b). Darwin Port Corporation received the highest number of commercial vessel calls for the year, accommodating 3115 visits (Ports Australia 2014b). Exceptions to commercial shipping growth are harbours where urban populations have pushed out trade (e.g. Sydney Harbour), or where activities are transitioning from industrial to recreational (Mayer-Pinto et al. 2015) There is a need for larger spatial- and temporal-scale assessments of vessel and infrastructure pressures using a consistent approach.

Recreational vessel pressure is related to both the number of vessels and the mechanism of storage. In Sydney Harbour, recreational boat density has increased at a rate of approximately 2 per cent per year, with additional moorings needed to secure boats when not in use. Almost 22,400 registered recreational vessels are expected for the harbour by 2021, which represents an increase of more than 5000 from a 2013 baseline (Transport for NSW 2013). Moorings affect the seabed because their attached chains scour the sediment, often disturbing seagrass and sediment infauna. Seagrass-friendly moorings (those without chains to disturb the seabed) have been installed at some locations, but still represent the minority of moorings in Australia.

Pressures related to vessel operations in coastal waters include propeller damage, wash, noise, debris, leaching of antifouling paints, oil spills, animal strikes, sediment resuspension, anchor drag, and acting as vectors for the transport of introduced species. The activities of vessels are often less environmentally damaging than their associated infrastructure, although regular resuspension of sediments from engine activity can cause a localised chronic impact in shallow areas of high traffic (Knott et al. 2009). The environmental impacts of infrastructure and capital works to support vessels are discussed in Artificial structures and Dredging. Chronic impacts have received relatively limited research, and more studies are required to understand the potential for ports to disrupt connectivity and ecosystem functioning along coastlines.

In the short term, present pressures are likely to increase as vessel activity and port size continue to expand to accommodate increasing trade and vessel numbers. There are opportunities to develop and adopt better practice to reduce environmental impacts, and a few notable rehabilitation works have occurred on the mid-north coast of New South Wales and the Swan River of Western Australia. The long-term outlook depends on climate change and the economic situation for Australia, particularly the state of iron ore and coal industries (see Mining), and activities that increase agricultural trade resulting from the northern Australia Development agenda (Australian Government 2015). Current management practices and procedures of ports need to be adapted to accommodate future consequences of climate change (Ng et al. 2013).

Invasive species (aquatic)

Estuarine and marine non-native species are typically introduced and spread through coastal waters by vessel movements (see Vessel activity and infrastructure) and, to a lesser extent, the aquarium trade and aquaculture (Minchin 2007, Savini et al. 2010). Once introduced, some non-native species successfully spread and increase in abundance, with potentially devastating consequences for native biodiversity. Not all non-native species become pests, but when they do, they are classified as invasive.

Invasive species often occur in high proportions on artificial substrates (see Artificial structures) (Dafforn et al. 2012, Airoldi et al. 2015) and introduced diseases are one of the main pressures on the aquaculture industry (see Aquaculture). Although there are numerous historical and recent invaders to Australian coastal waters, only a restricted set of conspicuous invasive species are well studied, and very little is known about impacts. Rarely do studies of invasive species examine impacts on ecological processes or the cumulative impacts of co-occurring invasive species.

There have been relatively few new incursions of known invasive species recorded in New South Wales in the past 5 years, and a decline in both the range and abundance of the invasive marine alga Caulerpa taxifolia. European fan worm (Sabella spallanzanii) invaded Botany Bay in 2013; since that time, 10 individuals have been found and removed. The Barker Inlet and the Port River estuary of South Australia have rising abundances of invasive European shore crabs (Carcinus maenas). The colonial ascidian (Didemnum perlucidum) has extensively spread throughout Western Australia in the past 5 years and is assumed to have detrimental impacts on ecological processes (Muñoz & McDonald 2014). Tasmania has incurred substantial ecological impacts from a range of invasive species, including the northern Pacific starfish (Asterias amurensis) and Japanese kelp (Undaria pinnatifida) (Valentine & Johnson 2003), although both of these established before 2011. In Victoria, monitoring and transport modelling has shown that A. amurensis larvae are being transported and spread out of Port Phillip Bay, expanding the invasive species’ range along the south-east coast and even establishing in pristine or remote environments such as Tidal River (Hirst et al. 2013).

The technical background for invasive species risk management is strong in Australia, and is the basis for many national and state biosecurity and management frameworks. However, this work needs to be updated to account for shifting likelihoods and risk profiles across regions and environments. Many government agencies have plans to deal with potentially invasive species once they are detected, but there are little baseline data to determine if a species is non-native, and a robust, coordinated research and monitoring effort to detect invaders and determine their environmental impacts does not exist. Ballast water regulations have been in effect for some time, but, until recently, Australia lacked national biofouling regulations.

The Biosecurity Act 2015 came into effect in June 2016 to replace the Quarantine Act 1908, with the intention to modernise national biosecurity and address some of these issues. Deficiency in data collection limits our ability to manage invaders and perpetuates the assumptions that there are few new incursions and that many invaders do not cause environmental impacts. Scientific studies on invasive species should consider the unique Australian environmental context, and be reported in terms that are interpretable in a management context. Marine biosecurity is a large-scale and diverse Australian issue, but is centrally underfunded and therefore requires effective communication and cooperation among researchers and agencies.

Pre-emptive management of invasive species involves:

• understanding, monitoring and regulating important vectors of introduction and spread
• limiting the suitability of early entry points for establishment (e.g. pollution and artificial structures)
• increasing the capacity to identify invasive species
• increasing ecosystem resilience by reducing other pressures.

The short-term outlook for invasive species in coastal waters is one of increasing rates of introduction, establishment opportunities and impacts. In the long term, increasing pressures from invasive species related to increased connectivity through vessel activity, climate change, pollution, reduced native resilience, and disturbances from coastal development and population growth, may outweigh potential advances in mitigation.

Diseases, infestations and fish kills

In Australia, there are 49 reportable aquatic diseases (23 for finfish, 13 for molluscs, 11 for crustaceans, 2 for amphibians), 34 of which are exotic (DAWR 2015). Some of these have had significant impacts on native species, such as the chitrid fungus Batrachochytrium dendrobatidis, which affects frogs in coastal areas. To aid reporting of disease occurrences, the Australian Government Department of Agriculture and Water Resources has developed a field guide to identify aquatic diseases. New diseases occur intermittently, but many reported mass mortality events are of unknown cause and most evidence is anecdotal. In New South Wales between 1970 and 2010, 38 per cent of fish kills were unattributed. The primary cause of many fish kills may not be infectious disease, but rather environmental conditions, particularly hypoxia (extremely low oxygen; see Coastal low-oxygen dead zones).

In New South Wales, mitigation programs are broadly implemented and well regulated, although damaging epizootics and new diseases (e.g. POMS) continue to occur. Most other notifiable diseases appeared stable during the past 5 years in New South Wales. In Victoria, the last outbreak of abalone viral ganglioneuritis was in 2010, but it was detected in a commercial population in Tasmania in 2011. Tasmania experienced an outbreak of POMS (Gibson 2016) in 2016, and a recent major fish kill of undetermined cause was seen in the Scamander River. In Western Australia, several fish kills of undetermined cause occurred in 2015, and abalone in South Australia continue to be affected by disease.

The National Aquaculture Statement and AQUAPLAN outline the national objectives for managing aquatic animal health relevant to aquaculture, commercial fisheries, recreational fisheries, the ornamental fish industry, tourism and the environment. Reporting is conducted on fish kills and notifiable diseases at a national level and in all states; however, data are generally inaccessible, lack detail and are not collaborated on at a national level. This hinders detection of outbreak trends, as does confounding by changes in report efficiency, diagnostics and regulation. The most detailed information comes from the fisheries and aquaculture industries (see Aquaculture) and World Organisation for Animal Health reports. AQUAVETPLAN, Australia’s Aquatic Veterinary Emergency Plan, outlines emergency response procedures for disease threats to Australia.

Introduction of diseases is an ongoing issue, with introductions potentially increasing in frequency. Climate change and the general decline in environmental conditions may amplify problems of disease, infestation and fish kills.

Algal blooms

Many algal blooms, which include blooms of phytoplankton, epiphytic algae and macroalgae, are beneficial natural events that provide food for invertebrates and fish. Harmful algal blooms, on the other hand, can have significant impacts on the environment, tourism, aquaculture and human health. They can de-oxygenate the water, affecting other organisms (e.g. seagrass and their associated communities) and reducing water quality. Toxins produced by the algae can bioaccumulate through the food web and be problematic for fisheries and aquaculture. Distinctive algal blooms, such as ‘red tides’, can close popular recreational areas (e.g. Bondi Beach) for extended periods of time. Harmful algal blooms have long been noted in Australian coastal waters. Early records include the toxigenic cyanobacterium Nodularia spumigena bloom in Lake Alexandrina in South Australia that killed cattle (Francis 1878), and the Scrippsiella trochoidea bloom in Sydney Harbour that caused oxygen depletion (Whitelegge 1891).

A primary driver of algal blooms in freshwater systems is poor water quality, such as occurs during drought and reduced flow, and increased organic enrichment as a result of upstream development and agriculture. Some bloom trends may be related to warmer waters associated with climate change (O’Neil et al. 2012), others to human transport via ships’ ballast water (Smayda 2007), but few can be definitively attributed to urbanisation. Many coastal algal blooms are more driven by water column stratification than by nutrients. Determining trends for harmful algal bloom frequency is confounded by an increase in reporting that has occurred with the growth of aquaculture.

Monitoring for blooms is handled by the states and territories, and effort varies around Australia, with phytoplankton data collection generally concentrated around large cities. Currently, there is no national-level synthesis of information on estuarine algal blooms, although an Australian phytoplankton database has recently been established (Davies 2016). Collaboration between state and territory agencies needs to be improved and data need to be made more easily accessible.

The general consensus is that freshwater environments globally are experiencing increased blooms of toxic cyanobacteria, but, apart from certain regional events, there is no clear evidence of an Australia-wide increase in blooms in major estuaries. New South Wales, South Australia and Tasmania have reasonably good microalgae monitoring, from which has emerged a trend of increasingly common algal blooms. The red-tide (nontoxic) dinoflagellate Noctiluca scintillans has expanded its range from the early 2000s from New South Wales to South Australia, Tasmania, Western Australia and Queensland (McLeod et al. 2012). Blooms of the dinoflagellate Alexandrium tamarense in Tasmania in 2015–16 were the largest (200 kilometres in diameter) and most toxic on record. These microalgae produce a paralytic shellfish toxin that closed the shellfish industry on the east coast of Tasmania for periods of weeks to months (see Diseases, infestations and fish kills). Changes in blooms in Tasmania are putatively linked to climate, whereas there is some evidence of changes in the seasonal bloom period in Sydney coastal waters. Monitoring is currently inadequate in the Northern Territory, Victoria, Western Australia, Queensland and remote areas of South Australia. In 2014–15 in Queensland, a ciguatera fish poisoning event was related to Gambierdiscus abundance. In Western Australia, deterioration of the Swan River is primarily because of reduced rainfall, which may increase the risk of algal blooms.

Sampling is usually not frequent enough to allow rapid response to blooms or to detect all outbreaks. Information is limited to a set of well-known species, and Australia is rapidly losing taxonomic expertise. A pressing issue is determining which bloom-forming species are in Australia and the conditions under which blooms of a particular species produce toxins that are harmful to aquaculture, fishing, humans, wildlife or stock (Hallegraeff 2016).

In the short term, algal blooms are expected to remain stable or worsen, depending on the decline of water quality from eutrophication and drought. Algal blooms may spread into new areas and raise immediate concern, although this should be short lived unless blooms recur. Increased water flows, whether naturally or through regulated environmental flows, should help to improve water quality and hence decrease the occurrences of algal blooms. The long-term outlook for algal blooms depends on the management of catchment (in particular, agriculture), freshwater and estuarine conditions, and the climate variability (i.e. drought periods).

Jellyfish blooms

Jellyfish are an integral component of healthy marine ecosystems and provide important ecosystem services. However, jellyfish blooms also have the potential to interfere with industry and recreational use of the coast (Purcell et al. 2007) by stinging humans, clogging intake valves (e.g. for mining and desalination plants), and disrupting fishing and aquaculture activities. Almost no data have been collected on jellyfish populations or their distributions to allow confident assessments on their current state, or to detect trends from background natural population cycles operating on 10–20-year scales.

Anthropogenic modification of coastal waterways can facilitate jellyfish blooms in several ways. Artificial structures may increase recruitment of early life stages of jellyfish (Duarte et al. 2012), and overfishing may release top-down pressure on jellyfish (Purcell & Arai 2001). Eutrophication may facilitate blooms, since increased availability of food increases reproduction rates of plankton, and this may benefit jellyfish (Stibor & Tokle 2003). Rising temperatures may also favour jellyfish by increasing fecundity and reducing time until strobilation (reproduction).

In Victoria, 20 years of monitoring suggests stable blue blubber (Catostylus mosaicus) abundance in Port Phillip Bay, with indications of a natural population cycle during this period. Similarly, in Moreton Bay in Queensland, monitoring indicates approximately 5–7-year population cycles of blue blubber. Limited sting data indicate a southwards range expansion of Irukandji jellyfish in Queensland and Western Australia, although sting data are not a reliable proxy for jellyfish abundance since they are confounded by the number of tourists and swimmers. In New South Wales, South Australia, Western Australia, Tasmania and the Northern Territory, there are no long-term quantitative data about jellyfish population changes.

Predictions of blooms require further research on jellyfish lifecycles and population drivers (both natural and anthropogenic), and monitoring on a timescale of several decades would be necessary to infer trends over and above natural cycles.

Coastal low-oxygen dead zones

Low-oxygen dead zones, also known as hypoxic events, are caused by oxygen depletion during eutrophication (Diaz & Rosenberg 2008). This occurs when excess nutrients enter coastal areas (e.g. during flood events) and cause algae to flourish to unnatural levels (see Nutrient pollution). When these algae die and are decomposed by microorganisms, oxygen is depleted to the extent that most other animals cannot survive (Breitburg et al. 2009). Coastal hypoxic events in Australia are currently restricted to estuaries (particularly salt-wedge estuaries), and are spatially and temporally variable. They are much less common in Australia than in other parts of the world, such as Europe. The major difficulty in managing coastal low-oxygen dead zones is understanding their cause, then addressing what are usually large-scale and intractable drivers.

In New South Wales, coastal dead zones do occur but are short-lived events. They tend to follow flooding of acid sulfate soils in drained agricultural or pastoral lands. Hypoxic events may result in total deoxygenation of tens of kilometres of river and subsequent fish deaths, as has occurred in both the Richmond and Hunter rivers. Less frequent are nonlethal deoxygenation events in intermittent lagoons, following freshwater stratification.

In 2010, the Swan–Canning Estuary in Western Australia experienced hypoxia after an extreme storm and heavy run-off, causing impacts on macroinvertebrate assemblages that persisted until hypoxia had eased (Tweedley et al. 2015). This event highlights the vulnerability of estuaries with small tides and long residence times, and there is a continuing trend of deoxygenation in intermittent lagoons in the south-west. Victoria has annual (natural) deoxygenation in intermittent estuaries in summer, and some areas in the Derwent Estuary of Tasmania suffer from hypoxia.