The status of marine biodiversity has been assessed by examining marine habitat quality, the species and populations, and the ecological processes that support the species and populations. These assessments of marine biodiversity are summarised for each region (the criteria used and detailed results are available on the SoE website^b) and aggregated into a single national assessment and report card for biodiversity.

The overall assessment of biodiversity found that the north and north-west regions are in very good condition, the east and south-west regions are in good condition, and the south-east region is in poor condition, although bordering on good (Figure 6.10).

Quality of habitats for species

Good-quality habitat is essential to support species populations and to allow natural ecological processes to operate. Habitat quality is defined using structural and functional intactness, relative to the conditions at the time of European settlement of Australia.

This section reports at the national level on our best understanding of the status and trends of marine habitat quality in 21 types of habitats that occur broadly and in more than one region, and 60 habitat types that occur principally in only one region.

South-west region

The habitats of the south-west region are overall in good condition. There are, however, a number of localised coastal areas of historical heavy impact where the effects remain—these include pollution and dredging of seagrass beds in Cockburn Sound, Perth; pollution-induced losses of seagrasses in Gulf St Vincent, Adelaide; and pollution of Albany harbours in Western Australia. Away from areas of coastal development or river run-off, many habitats remain in good condition. Water conditions overall are very good, particularly away from the shoreline. Conditions of habitats of the estuaries and lagoons of this region are considered overall to be very poor.

Seagrass beds are a dominant habitat in the south-west of Australia, occurring in many intertidal and subtidal areas of coastal waters and estuaries, and in offshore locations down to 50 metres depth. Seagrasses provide important habitat for many fish and invertebrate species, and they host important parts of the lifecycle of a number of fished species. Although two species of seagrass (Posidonia sinuosa and P. australis) are considered threatened or near-threatened with extinction,²⁹ in most places in this region seagrasses are in very good condition.

North-west region

The habitats of the north-west region are overall in very good condition. Much of this region is very remote (particularly the north) and, as a result, many habitats are considered to be very good and in nearly pristine condition. These include the large gulfs and bays, fringing coral reefs, and seagrass and algal bed systems of the Kimberley, and most of the offshore shoals and islands, canyons and shelf-break ecosystems of the region. Some of the world’s most extensive undisturbed tropical and subtropical habitats occur in the shallow waters of the Kimberley, Ningaloo Reef, Roebuck Bay and Shark Bay. Nonetheless, there are localised areas where the habitats are in very poor condition, such as near Dampier, Port Hedland and Onslow, where ports and shipping activities have heavily impacted coral and mangrove habitats. Offshore habitats are generally in good condition, although the deepwater corals and sponges of the North West Shelf are still considered to be heavily degraded and only slowly recovering from the extensive impacts of historical trawling, and some offshore islands have been heavily impacted by foreign fishing.

In the Kimberley, there are 343 islands with more than 20 hectares of land above mean high water, and many more smaller islands.³⁰ Almost all the islands have fringing reef systems of complex hard coral and algal (rhodolith) habitats. Most of these are remote from human influences and in very good and near-pristine condition.

North region

Like the north-west, the habitats of the north region are also remote and pristine tropical habitats, and most are considered to be in very good condition. These include the nearshore shallow-water marine systems, the extensive shoreline wetlands, and the bays and gulfs of the region. However, the pressures of coastal development are evident in some areas, such as Darwin Harbour and Melville Bay (Nhulunbuy, Northern Territory), where a localised, biologically dead area has been created by mining wastes. Most of the rivers are substantially unmodified. Exceptions are the Ord River, which is heavily modified by the Ord River Dam, resulting in substantial impacts on the estuarine habitats of the delta in Cambridge Gulf; and the Macarthur River, which is modified by mining.

East region

The east region includes the Great Barrier Reef, Torres Strait, the Coral Sea plateau and islands, Fraser Island, Sydney Harbour, Jervis Bay, and the many smaller islands, bays and estuaries of the New South Wales coast. Habitats of the northern part of the region are considered to be in good condition overall, despite considerable pressure from land-based sources of pollution. The Great Barrier Reef region has been considered in detail, and a condition assessment is presented in the Great Barrier Reef outlook report 2009.³¹ However, the habitats of the central and southern part of the region are more degraded, and many are considered to be poor. This is mainly the result of population pressures in coastal areas (such as in south-east Queensland and northern New South Wales), beach modifications, loss of major areas of seagrass and corals, historical effects of heavy trawling on the continental shelf, and major modification of rivers, some of which (such as the Tweed River) have significantly modified catchments for agriculture and altered freshwater flow regimes feeding to the estuaries and bays. Herbicides have been found in all water sampling sites in the inshore waters of the Great Barrier Reef and, in some places, are approaching levels that may have significant impacts on coral and other marine life.³² In New South Wales, the seagrass Posidonia australis is proposed to be declared as an endangered species in six areas where it formerly occurred widely, because of various impacts (such as dredging and pollution) over the past decades.³³

South-east region

The overall quality of habitat in the south-east region is poor; the pressures of population, shipping, fishing and development in many places have degraded habitats of inshore waters, bays and estuaries. This is the only region where a habitat type has been made functionally extinct by human activities—the oyster reef beds that formerly dominated a number of the estuaries and small bays were exterminated by mining and fishing practices by the end of the 1800s. Seven of the 11 formerly existing oyster reefs assessed are functionally extinct, while the remaining 4 were assessed as having more than 90% of their area lost.³⁴ This has had a significant impact on ecological systems, reducing habitat for many other species and probably greatly affecting the overall water filtering (purification) capacity of these affected areas and their capacity to assimilate nutrient inputs.

Populations of species and groups of species

This section reports on our best understanding at the national level of the status and trends of 31 major populations and groups of marine species, including threatened species. Condition of the populations of species and groups of species is defined by the extent to which populations have declined because of human activities, relative to their condition at the time of European settlement of Australia. There has been no previous national synthesis of species condition, and the assessments reported here are derived from the national marine condition assessment workshops. The criteria used in the workshops are available on the SoE website.^c

Species are threatened mainly by direct exploitation and by loss of, or changes in, their habitats. Future assessments of the condition of marine species will also need to consider the impacts of climate change on both the inherent biological properties of individual species and their preferred habitats. To enable accurate reporting of population conditions and trends, these future assessments will need to be conducted using more holistic ecological approaches to population condition assessment, such as those outlined for the coral trout and the butterflyfish in Box 6.5.³⁵

South-west region

The populations of 16 of the 29 species and species groups assessed were found to be in poor or very poor condition in the south-west region—these were mainly the large species for which there was enough knowledge to be able to make a judgement. Species and groups considered to be in poor condition include exploited sharks and rays, whale sharks, great white sharks, exploited tuna and billfish, southern bluefin tuna, exploited species of reef fish, seabed species of the inner shelf, migratory seabirds, dolphins and porpoises, seals and sea lions, and baleen and toothed whales (although humpback whale populations are considered to be in good condition and strongly recovering from historical hunting). Invertebrate species, seahorses and their relatives, small pelagic fish, and sharks and rays that are not targeted by commercial or recreational fishers are considered to be in good condition.

Australian sea lions are endemic to this region. After intense hunting in the 1800s, their population still does not show any significant recovery. Increases have been documented only at Dangerous Reef in South Australia. Breeding colonies are substantially isolated from each other, and population recovery will continue to be a very slow process and subject to pressures of climate change and incidental mortality in fisheries.

North-west region

The populations of 15 of the 21 species and species groups assessed in the north-west region were found to be in good or very good condition. These include most of the shelf invertebrate species, the corals and shoreline species, dugongs, dolphins, humpback whales, crocodiles and sea snakes. Most of these groups that are in good or very good condition are considered to have stable populations. Nonetheless, the sea snakes at Ashmore Reef and the larger species of tuna and billfish across the region were considered to be in very poor condition. Also, across the region, large predatory reef fish (species targeted in commercial and recreational fisheries) were considered to be in poor condition overall.

Cod have been heavily fished in most of the southern parts of this region, including at Ningaloo Reef. Oral histories indicate that the populations that once existed are now largely gone, and the large, old fish no longer exist:

…cods were everywhere—there were hundreds of them there, and they were giving me trouble every day. One snuck up behind me and took a full bag of crayfish—and when I say a full bag I mean about eighty pounds of crayfish. When I looked around there was this big monster of a cod there and he had about a quarter of my bag in his mouth. Farinaccio³⁶

North region

The species and their populations in the north region are considered to be overall in very good condition—14 of the 17 species and species groups were assessed as being in good or very good condition. The remoteness of the region and lack of major pressures indicate, with a high level of certainty, that many species and their populations have been only slightly changed from their likely condition at the time of European settlement. Nonetheless, a number of exploited populations could not be assessed, and their condition is likely to range from good to poor. Turtles and migratory seabird populations were considered to be in poor condition, mostly because of pressures on their populations outside the region, including internationally. Other species that occur in this region, such as the Indo–Pacific humpback dolphin and the Australian snubfin dolphin, are listed by the International Union for Conservation of Nature (IUCN) as near threatened.

East region

The species populations in the east region are overall in poor condition—20 of the 29 species and species groups assessed were in poor or very poor condition. The populations considered to be in the worst condition include the invertebrates and plant species of the dunes, shoreline and shallow inner-shelf waters; fish of the shallow-water reefs; migratory wading birds; sea snakes; dugongs; turtles and whales. In some places, hard corals are considered to be in very poor condition. Within the Great Barrier Reef Marine Park, some of these populations are considered to be in good condition. The invertebrate species of the outer shelf and slope, the species of sharks and rays that are not targeted by fishing, and remote areas of the Coral Sea are considered to be in good condition across this region.

South-east region

The species populations of the south-east region are in poor condition overall—14 of the 24 species and species groups were assessed as being in poor or very poor condition. Populations considered to be in poor to very poor condition across the region include major predator species (such as great white sharks and southern bluefin tuna), species of the outer shelf and upper slope where intensive fishing was conducted in earlier years, inshore reef fish species, and species of seagrass and mangroves. The Oceania (south-west Pacific) subpopulation of humpback whales remains IUCN-listed as endangered.³⁷

Ecological processes

This section reports on our best understanding at the national level of the status and trends of the 15 major national-scale ecological processes that operate in the regions and the effects of human activities on them. The processes assessed here include aspects such as migration pathways (are human activities interrupting the normal migration routes of animals between their feeding and breeding grounds?), and trophic (food web) structures of the ecosystems (does the abundance and distribution of the species among primary producers, secondary producers and predators reflect the natural structure and rates of interaction?). Condition of the processes is defined by the extent to which they have declined because of human activities, relative to their condition at the time of European settlement of Australia (further details of the criteria are on the SoE website^d).

South-west region

The main ecological processes for the south-west region are in good condition, including unimpeded physical pathways for migration, maintenance of most feeding grounds, and maintenance of the main sources of water column productivity, reef building processes and symbiotic relationships across the region. However, coastal development has had major impacts on recruitment and settlement processes for fish and invertebrate coastal species across the region; and nesting, roosting and nursery sites for seabirds. Predation as a process has been severely affected by the removal of top predators from across the region. These impacts continue to increase.

North-west region

Like the south-west, the main ecological processes in the north-west region are in good condition overall. This is partly because the two regions are closely connected by the Leeuwin Current, and because some of the same threats apply to both regions. In parts of both regions that are remote from human influences, some of the ecological processes (such as offshore benthic productivity, symbiosis and reef building) are considered to be in very good condition. However, in other areas, removal of top predators has affected predation as a process, which is considered to be in poor condition and significantly affects ecosystem function in some areas of this region.

North region

The ecological processes in the north region overall are in very good condition, and there are considered to be few significant ecological changes to the main processes of the region as a result of human activities. However, in the offshore areas, the trophic structures and relationships are considered to be poor across the region, and very poor in some areas. This has resulted from excessive fishing pressures, including illegal fishing and the extensive impact of discarded bycatch and related wastes. Top predators have been heavily fished, and impacts in international waters and adjacent areas are likely to have a flow-on effect on the trophic structures of this region.

East region

The ecological processes of the east region are considered to be in good condition overall. These include processes such as the maintenance of migration pathways; availability of nesting, roosting and feeding grounds; reef building; activities of herbivores; and algal-derived calcification processes. However, the flooding cycles of the coastal wetlands are considered to in very poor condition, with substantial changes across a wide area, resulting in serious effects on ecosystem functions. Hydrological regimes altered by land use, coastal engineering, water harvest and flood protection have substantially altered the seasonal habitat cycles in wetlands.

South-east region

The ecological processes of the south-east region are considered overall to be in very good condition. However, the reef building process has been heavily reduced and is in poor condition. The loss of oyster reefs from shallow inshore waters is widespread (these reefs are considered to be functionally extinct), and trawling has removed much of the deepwater bryozoan reef in fishable depths.