The condition of Australian estuaries and bays, and coastal freshwater lakes and lagoons is covered in detail in the Coasts report. The Marine environment report provides a detailed assessment of the state and trends of marine organisms. We provide a high-level summary here.

Three coastal or marine ecosystems were listed as threatened ecological communities under the EPBC Act during the past 5 years:

• the Giant Kelp Marine Forests of South East Australia (2012) and Posidonia australis seagrass meadows of the Manning–Hawkesbury ecoregion (2015) were listed as endangered
• Subtropical and Temperate Coastal Saltmarsh (2013) was listed as vulnerable.

The primary threats affecting the Giant Kelp Marine Forests are the increase in sea surface temperatures associated with the southwards penetration of the East Australian Current, and the corresponding range expansion of kelp-grazing sea urchins. The cumulative consequences of coastal development (e.g. clearing and human-induced habitat modification), and invasive species, are considered key threats to the P. australis seagrass meadows and the Subtropical and Temperate Coastal Saltmarsh communities.

A range of habitats and communities—from the nearshore to the abyss, and from the seabed to the water column—were assessed for their current state and recent trends in the Marine environment report Most were in good condition, and trends ranged from stable to improving, where they could be assessed. However, the condition of canyons, seamounts and coral reefs ranged from good to poor, depending on the specific geographic region. For example, severe storms, bleaching and crown-of-thorns starfish have affected eastern reefs, whereas many regions in the north-west have been affected by bleaching. Habitats and communities in the Great Barrier Reef to the end of 2015 are considered to range from poor and worsening condition (corals) to good and stable condition (macroalgae, offshore banks and shoals) (GBRMPA 2014). The ecosystem encompassing ‘Fringing reefs—temperate rocky reefs’ was classed as poor and worsening; warm-water events and overgrazing by sea urchins are negatively affecting some temperate reef habitats. Trends were generally noted to be associated with limited confidence for many habitats.

Most species groups assessed are regarded as being in good condition overall, although information is lacking to assess the condition or trend of some invertebrate groups. Trends are stable or improving for most fish species, except inner shelf reef species, which are in poor condition and worsening, similar to temperate rocky reef and coral reef habitats.

In addition, some species:

• have improved from past declines (e.g. long-nosed fur seals—Arctocephalus forsteri, southern Great Barrier Reef green turtles—Chelonia mydas, humpback whales—Megaptera novaeangliae, orange roughy—Hoplostethus atlanticus)
• are stable (e.g. mesopelagic and epipelagic fish species, shy albatross—Thalassarche cauta)
• have declined as a result of cumulative impacts associated with high fishing mortality, bycatch within fisheries and climate change (e.g. flesh-footed shearwater—Puffinus carneipes, Australian sea lion—Neophoca cinerea, north Queensland hawksbill turtle—Eretmochelys imbricata, demersal shark species).

Dugong populations in the southern Great Barrier Reef declined to very low levels during the past 50 years, with the aerial survey in 2011 showing the lowest numbers since the surveys began in 1986 (Sobtzick et al. 2012, 2015). In 2015, the Australian Government committed $5.3 million across 3 years for delivery of a Dugong and Turtle Protection Plan, including a Specialised Indigenous Ranger Program for strengthened enforcement and compliance, and an Australian Crime Commission investigation into the illegal poaching, transportation and trade of turtle and dugong meat in the Great Barrier Reef and Torres Strait. Other measures undertaken by local Indigenous people along the length of the Reef include a variety of sea Country management arrangements, including Traditional Use of Marine Resources Agreements and Marine Park Indigenous Land Use Agreements.

Large numbers of species and species groups are not regularly monitored or monitored at all, and, as a result, their status is unknown and recent trends are unclear. Trends were unclear for sharks and rays, most seabirds, sea snakes, some marine turtles and most marine mammals.

There is broad agreement on the current very poor state and deteriorating trend of shorebirds in the past 5 years (see Box BIO13), with consensus and evidence pointing to the causes as habitat loss, habitat degradation and harvest of prey, particularly in east Asia. Current trends in shorebird populations are described in detail in the Coasts report.

Jurisdictional reporting on marine species and ecosystems

The state of marine ecosystems is highly variable, but the jurisdictions report that many systems are in good condition. Trend is generally not known, and the reliability of information for many systems is also limited.

New South Wales

• Key trends:
  • Forty-one marine species and 1 marine population are currently listed as threatened, including some presumed extinct. Information on the status of marine species is generally not as good as that for terrestrial species.
  • Significant losses of aquatic vegetation have occurred since European settlement; however, information is too limited to assess recent changes. Ongoing losses of seagrass communities tend to be small, and many relate to localised climatic events.
• Assessment grade and adequacy of information:
  • Distribution of rocky reef covering biota: grade—good; trend—unknown; information availability—limited.
  • Distribution of estuarine macrophytes: grade—moderate; trend—unknown; information availability—limited.
  • Levels of estuarine catchment disturbance: grade—moderate; trend—increasing impact; information availability—limited.

Queensland

• Key trends:
  • Sediment, nutrients and chemicals, and litter are the major catchment pressures that affect Queensland estuaries and marine environments, but these vary in their relative importance between regions.
  • Changes to coastal habitat and reductions in connectivity are having an increasing effect on the region’s ecosystems.
  • More than 96 per cent of the pre-European settlement extent of estuarine wetlands in Queensland remained in 2013. Changes in the extent of estuarine wetlands in Queensland have been monitored since 2001. The highest rate of estuarine wetland loss was recorded during 2009–13 (0.03 per cent), mostly in the North East Coast drainage division.
  • Of the 2 broad estuarine wetland types—mangrove and saltmarsh/salt flat—the greatest ongoing losses have occurred in saltmarsh and salt flats in the North East Coast drainage division, yet more than 95 per cent remain intact.
  • Thirty-six per cent of estuarine wetlands across Queensland are within areas of managed protection, which often overlap; of these, 26 per cent are in declared fish habitat area, 12 per cent are in highly protected marine park zones, and only 5 per cent are in protected areas.
  • About 17 per cent—or 1.8 million hectares—of Queensland’s total marine wetlands are in highly protected marine park zones or a declared fish habitat area.
  • Queensland remains largely free from invasive non-native marine flora and fauna species (marine pests), despite a high possibility of introduction through international shipping activity.
  • The volume and load of nitrogen and phosphorus released from coastal sewage treatment plants into waterways in Queensland have remained relatively constant since 2010, except for a significant reduction in both volume and nitrogen loads released in 2014. Phosphorus loads increased in south-east Queensland in 2014, most likely because of reduced water recycling from advanced water treatment plants.
  • For the Great Barrier Reef
    • climate-related variables are already having an effect, and are predicted to continue to have far-reaching consequences for the Reef ecosystem
    • direct use of the region is a significant economic contributor, and its impact on the region’s ecosystem is projected to increase with population growth
    • declining marine water quality is one of the most significant threats to the Reef; however, agricultural practices are improving, resulting in reductions in land-based run-off entering the region
    • evidence suggests that increased nutrient loads contribute to more frequent outbreaks of crown-of-thorns starfish—a major predator of coral—resulting in coral cover decline.
• Assessment grade and adequacy of information:
  • Assessment grades vary from one report card to another, and across time periods.
  • Most of Queensland’s key fish stocks are considered sustainable.
  • At a Reef-wide scale, most ecological processes are considered to be in good condition; however, the inshore southern two-thirds of the region are in decline.
  • Queensland is well covered by water quality monitoring at different timescales, from annual report cards in coastal areas to less frequent monitoring in more remote regions. Areas such as the Gulf of Carpentaria and parts of the Murray–Darling Basin have not yet been covered, but will be addressed in future programs.

Victoria

• Key trends:
  • Monitoring has shown some positive changes in marine and coastal communities as a result of the establishment of marine parks and sanctuaries. However, changes in ecological community structure have also been observed, such as a decrease in the key habitat-forming seaweed in Port Phillip Heads Marine National Park, increased presence of pests such as the long-spined sea urchin (Centrostephanus rodgersii), decline of the southern rock lobster population, and a decline in broad-leaf seagrass (Posidonia australis).
  • Between 2007 and 2013, 6 marine and coastal bird species declined in status, and 2 bird species were added to the Advisory List because of decreasing populations. Only 1 species improved its threatened status during the past 5 years.
  • Assessment of threatened communities and species in marine environments is limited compared with terrestrial environments, particularly for marine flora, invertebrates and fish.
  • Marine and coastal ecosystems are under increased threat from invasive species.
• Assessment grade and adequacy of information:
  • Data on the condition of marine and coastal ecosystems are not gathered in a comprehensive manner. A lack of knowledge and understanding of marine systems is a major hindrance to the protection of marine biodiversity and the ability to report on its current condition.
  • Monitoring of invasive species remains poor, and is limited to Victoria’s commercial ports and harbours.
  • Few data are available on the ecological condition of estuaries, although it is evident that most of Victoria’s estuaries have degraded.
  • Marine and coastal health: grade—unknown; trend—unknown; data quality—poor.
  • Conservation of marine and coastal areas: grade—poor; trend—stable; data quality—good.
  • Marine and coastal biodiversity: grade—poor; trend—unknown; data quality—poor.

South Australia

• Key trends:
  • South Australian marine parks were established in November 2012, and restrictions on activities other than fishing began in March 2013. Fishing restrictions within marine parks took effect in October 2014.
  • In 2007, more than 90 per cent of mangroves were in good condition. Field surveys across the Eyre Peninsula NRM region in 2012 assessed the mangroves as being in good condition, with a score of 71 out of 100 (where 100 represents pristine, undisturbed condition). Trends in condition are unknown.
  • In 2007, more than 90 per cent of saltmarshes were in good condition. Trends in condition are unknown.
• Assessment grade and adequacy of information:
  • A monitoring, evaluation and reporting program has commenced, which will assess trends in the condition of the key ecological, environmental, cultural and socio-economic resources in each marine park.
  • The condition and trend of coastal dunes throughout the state are largely unknown. Studies of dune condition have not been undertaken in any NRM region.
  • Effectiveness of marine parks in protecting marine habitats and species: grade—good; trend—unknown; reliability of information—excellent.
  • The condition of coastal vegetation, estuaries and subtidal reefs has generally not been assessed in the reporting period. The most recent assessments given in the South Australian NRM report cards are
    • extent and condition of coastal dunes (2007): grade—unknown; trend—unknown; reliability of information—fair
    • extent and condition of mangroves (2007): grade—good; trend—unknown; reliability of information—good
    • extent and condition of saltmarshes (2007): grade—good; trend—unknown; reliability of information—good
    • extent and condition of seagrasses (2011): grade—unknown; trend—stable; reliability of information—good
    • condition of estuaries (2001): grade—poor; trend—unknown; reliability of information—fair
    • condition of subtidal reefs (2010): grade—unknown; trend—unknown; reliability of information—good.

Western Australia

• Key trends:
  • Western Australia has a network of marine parks and reserves across 13 of the state’s 19 marine bioregions.
  • The subtropical and temperate saltmarsh threatened ecological community has declined in extent through land clearing or reclamation, altered hydrology, eutrophication and/or grazing.
  • Most south-western estuaries are affected to some extent by eutrophication, with several areas showing signs of severe impact.
  • Coral condition in marine parks and reserves is generally good, although abnormally warm water during the 2011 La Niña event caused coral bleaching, and coral cover declined on some mid-latitude to high-latitude reefs. The strong El Niño event in 2016 increased water temperature, and caused coral bleaching on reefs along the Kimberley coast and at some offshore atolls.
  • The 2011 La Niña warm-water event and flooding from storms were associated with a decline in cover of some seagrass species in Shark Bay Marine Park. Seagrass in the Swan–Canning estuary is generally in good condition. Warm water from the 2011 La Niña and strong La Niña events in the following 2 years have also contributed to reduced coverage of kelp on mid-latitude reefs, although kelp communities are still in good condition in southern waters.
  • The condition of marine turtles is generally good, although many more years of data are required to understand the potential long-term impacts of pressures associated with major industrial developments in the Pilbara region. Long-term data at Ningaloo indicate that green, hawksbill and loggerhead turtles have stable nesting abundances, and fox predation on eggs has been reduced to less than 1 per cent.
  • Humpback whale numbers in the west coast breeding stock have increased significantly to around 30,000 animals, and this species was moved from the threatened species list to the specially protected/conservation dependent category in 2015.
  • Salinity is increasing in the Swan–Canning estuary system (1995–2011), consistent with increased tidal influence and reduced river flow (with drying climate). Associated stratification has resulted in an improved oxygen trend in downstream reaches, but a decreasing trend in upper reaches. Nutrient levels are stable in upper reaches, but chlorophyll-a has increased (2005–11), possibly because of increased light penetration. Fish communities in the estuary system are stable.
• Assessment grade and adequacy of information:
  • The Department of Parks and Wildlife monitors the condition of key ecological assets relative to anthropogenic pressures and the condition of some threatened marine species.
  • Condition of saltmarsh ecological community: grade—good to fair; trend—declining; reliability of information—moderate to fair.
  • Condition of corals: grade—good; trend—generally stable, although declining at some reefs; reliability of information—good.
  • Condition of seagrass and macroalgal communities: grade—good; trend—stable, although some are declining at some locations; reliability of information—good.
  • Condition of mangroves: grade—good; trend—stable; reliability of information—good.
  • Condition of intertidal reefs: grade—good; trend—unknown, because timeseries data are insufficient; reliability of information—good.
  • Condition of marine turtles: grade—good; trend—unknown, because long-lived species require long timeseries of data; reliability of information—fair.

Tasmania

• Key trends:
  • State coastal (and marine) areas have been divided into mesoscale bioregions, based on biogeographical spatial distribution of biological and physical characteristics. The coastline has been divided further into 20-kilometre segments, based on naturalness values (evaluated on aquatic species and marine water–dependent terrestrial species present). Most regions have ecological conditions classified as slightly to moderately disturbed, with some of these regions classified as having high ecological value (mostly adjacent to the south-west Tasmania World Heritage Area). A few isolated areas that have been affected by significant land-based activities are classified as highly disturbed.
  • Port Davey and associated Bathurst Harbour in south-west Tasmania represent one of the world’s most anomalous estuarine systems. The estuary contains several fragile deepwater invertebrate species growing at accessibly shallow depths; the reef habitats are susceptible to impacts and are of scientific importance. In 2011, the 2003 baseline survey of introduced marine pests was repeated at Port Davey. No target introduced marine pests were detected during the survey, which included collections made using benthic cores, diver video transects, diver searches, baited trapping, beach wrack searches, benthic phytoplankton cores and plankton net tows.
• Assessment grade and adequacy of information:
  • Limited coastal and marine ecosystem monitoring occurs outside sites used to assess impacts of activities, areas included in the Tamar and Derwent estuaries’ strategic monitoring programs, and areas monitored as part of baseline ecological monitoring for managing marine farms. However, all CSIRO data processed as part of determining site-specific guideline values for protecting aquatic ecosystems indicate water quality sufficient to support slightly to moderately affected ecological condition.
  • Marine and coastal health: grade—fair to good; trend—stable to declining, but generally unknown outside locations being assessed; data quality—good, but nearshore data are generally limited.
  • Conservation of marine and coastal areas: grade—fair to good; trend—stable to declining, but generally unknown outside locations being assessed; data quality—fair to good, but limited.
  • Effectiveness of marine parks in protecting marine habitats and species: grade—good; trend—unknown; reliability of information—good.
  • Marine and coastal biodiversity: grade—fair to good (outside affected zones); trend—stable to declining, but generally unknown outside locations being assessed; data quality—fair to good, but limited.
  • Estuarine health: grade—poor to good; trend—stable to declining, but generally unknown outside locations being assessed; data quality—good, but generally limited to Institute for Marine and Antarctic Studies data and site-specific assessment of regulated activities.

Northern Territory

• Key trends and adequacy of information:
  • Systematic assessment of dugong populations in the territory show that the major population in the Gulf of Carpentaria has remained stable since 1994.
  • Systematic monitoring of saltwater crocodiles in the territory shows a continuing recovery since protection from hunting in 1970, with populations in the major river systems either continuing to increase slowly or stabilising, and a gradual shift towards larger individuals.
  • Extensive dieback of mangroves occurred in the Gulf of Carpentaria during 2015–16, with around 7000 hectares affected. This is likely linked to poor wet-season rainfall combined with very high temperatures.
  • There is also some anecdotal evidence of coral bleaching in coastal territory waters during 2015–16.
• Assessment grade:
  • The environmental condition of Darwin Harbour is assessed and reported annually against 4 key water quality indicators. In 2015, all sites were assessed as having very good or excellent water quality, except for Buffalo Creek (very poor), which receives discharge from a sewage treatment plant.
  • Marine and estuarine ecosystems in the Northern Territory are generally in good ecological condition, although quantitative data for trends are sparse.