Ecosystems

Within the living fabric of Australia’s diverse landscapes and seascapes is a complex system of ecosystems of living organisms intertwined with the physical environment they inhabit. Ecosystems are the basis for life – they provide habitat, promote food chains and webs, and control ecological cycles and processes.

The disruption and degradation of ecosystems can lead to irreversible collapse, when key defining features and functions of the ecosystem are lost. At least 19 Australian ecosystems have been reported to show signs of collapse or near collapse, although none has yet collapsed across the entire distribution (Bergstrom et al. 2021). Ecosystems experiencing collapse span the Australian continent, and include Antarctic and subantarctic ecosystems.

Across Australia, our ecosystems contain elements that are vital for Indigenous people as food and medicine. It is estimated that around 4,000 different plant species are used, which is around 20% of named Australian vascular plants (Isaacs 1987 in Ens et al. 2017). Evidence from the Madjedbebe rock-shelter in northern Australia in the form of charred plant food remains dated to 65,000–53,000 years ago indicates that Australia’s earliest known human population exploited a range of plant foods, including those requiring processing (Florin et al. 2020). Many more plant species were used as materials for tools, shelter and ceremonial items.

Assessment Ecosystems

2021

Assessments of state range from poor to good
Assessments of trend range from deteriorating to stable

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Assessment Terrestrial ecosystems and native vegetation

2021

Environmental values of terrestrial ecosystems continue to decline as native vegetation and above-ground carbon stocks are lost through human pressures such as land-use practices and clearing.
Assessments of state range from poor to good
Assessments of trend are deteriorating
Related to United Nations Sustainable Development Goal target 13.2

Assessment Freshwater ecosystems

2021

Freshwater ecosystems have been significantly impacted by human activity, generally in the south; habitats have degraded; and breeding grounds and refuges have declined. Drought has had significant impacts on water-dependent ecosystems and culturally significant sites.
Assessments of state are poor
Assessments of trend range from deteriorating to stable
Related to United Nations Sustainable Development Goal targets 6.6, 15.1, 15.6

Assessment Marine and coastal ecosystems

2021

Most marine habitats and communities are in a good and stable condition; however, seamounts and reef ecosystems are in poor condition, reefs are deteriorating, and the reorganisation of communities and disruption of ecological connectivity as a result of climate change and cumulative impacts is increasingly apparent. Coastal ecosystems are generally in poor and deteriorating condition in the south-east. Traditional Owners assessed marine habitats and communities as generally in poor and deteriorating condition.
Assessments of state range from poor to very good
Assessments of trend range from deteriorating to stable
Related to United Nations Sustainable Development Goal targets 14.1, 14.2, 14.4, 14.5

Terrestrial ecosystems and native vegetation

Native vegetation is crucial for the health of Australia’s environment – it stabilises soil, supports beneficial pollinators and other animals, purifies water, stores carbon, and provides food and habitat for biodiversity. Vegetation and fungi together provide the foundation of the food chain for land-based ecosystems.

The Australian continent supports a vast array of ecosystem types, which have been aggregated at the national level into 89 bioregions and 419 subregions based on climate, geology, landform, native vegetation and species information, described in the Interim Biogeographic Regionalisation for Australia (Thackway & Cresswell 1995, DAWE 2021e). The bioregions and subregions are the reporting unit for assessing the level of protection in the National Reserve System (see Protected areas).

Historically, native vegetation has been cleared or degraded by human activity to enable other uses of the land; 13.2% of Australia’s native vegetation has been replaced by urban, production and extractive uses of the land (see Land clearing). Native vegetation has been mapped by each state and territory, and has been aggregated into 28 major native vegetation groups and 78 subgroups, through Australia’s National Vegetation Information System. Almost half of Australia’s major vegetation types have lost at least 20% of their original extent, and one (casuarina forests and woodlands) has lost more than 40% of its original extent. Woodlands have been extensively cleared, with only 53% of casuarina forests and woodlands, and 67% of the original eucalypt woodlands remaining (DAWE 2020b, DAWE 2020g).

From 2015 to 2019, nearly 290,000 hectares of primary forest was cleared and a further 343,000 hectares of secondary forest (regrowth) was re-cleared (DISER 2021e). In addition, extensive areas of sparse woody and nonwoody vegetation have been cleared and converted to other uses, principally pastures; the full extent of this conversion is not well documented. Clearing has been implicated in the listing of 60% of Australia’s threatened species under the EPBC Act (Kearney et al. 2018). The most intensively used areas of Australia have the most fragmented native vegetation, such as our major agricultural areas, and the urban and peri-urban areas of Australia’s major cities and towns.

Significant areas of native vegetation have been extensively impacted by the grazing activities of sheep and cattle, as well as the destructive activities of introduced species such as pigs, goats, camels, buffalo, horses and donkeys.

Changes to ecosystems from human influences can also result in subtle changes to our native species. For example, many species are highly sensitive to changes in water quality; in Moreton Bay in Queensland, the composition of the diatom community has shown distinct changes in relation to floods, increasing urbanisation and agriculture in the large catchment. The growth of bloom-forming marine planktonic diatoms has increased since the mid-20th century compared with the dominant benthic diatom. This transition is most likely due to a shift in the quality of run-off entering the bay; run-off events of the latter half of the century were characterised by increased fine sediment, nitrogen and pollutant loads (Coates-Marnane et al. 2021).

Most Australians live close to the coast, which puts immense pressure on our coastal ecosystems. The biodiverse coastal areas of south-eastern and south-western Australia continue to see a decline in dune vegetation and ecological function. For the whole of Australia, 11% of coastal dune vegetation from 2014 to 2019 was lost, mainly because of the 2019–20 bushfires (see Bushfires), land clearing and reduced rainfall. Coastal vegetation in northern and north-western Australia ranges from poor to good condition. Extensive transformation of native systems to monocultures of introduced species has occurred, as well as loss of significant zones of vegetation across large areas of tropical Australia due to the unseasonably dry wet season in 2019–20 that left coastal dunes exposed to erosion from high winds and cyclonic activity (Babcock et al. 2019b, Duke et al. 2020).

However, although clearing is ongoing, there is also investment in sustainable use and conservation of native vegetation, including efforts to manage and protect natural areas, and restoration of degraded landscapes.

Restoration efforts include those aimed at protecting and restoring our soils. The living part of soil is a critical part of every ecosystem, and is vital for maintaining fertility, species diversity and resilience in natural ecosystems (see Land). Soil biodiversity is increasingly recognised as being important for human health and wellbeing because healthy soils can suppress disease-causing soil organisms and positively influence the quality of food, air and water (Wall et al. 2015).

Freshwater ecosystems

In much of southern Australia, the greatest threat to freshwater ecosystems and biodiversity is the modification of water processes that has occurred as a result of changes to river and stream flow, surface water and groundwater extraction (primarily for agriculture), and land-use change. Altered water flows, of both surface water and groundwater, have also caused changes to water and soil quality, including salination, sedimentation, and acidification due to the exposure of sulfidic sediments (Capon et al. 2017). Other pressures include barriers to fish movement, invasive species, habitat loss and alteration, and commercial and recreational fishing (Koehn et al. 2020a).

Since 2016, periods of historically low rainfall have significantly affected inland water environments. Australia experienced its lowest-on-record 24-month rainfall period over 2018–20. Climatic extremes – our ‘droughts and flooding rains’ – are a natural feature of Australia’s hydrology. However, their impact on aquatic ecosystems and species is compounded by the continuing pressures of water extraction and development, loss of refugia and deteriorating catchment condition, which may themselves be amplified by climate change. Future changes in the global climate system are likely to have an even more profound impact on hydrology.

The overall assessment of Australia’s freshwater ecosystems in southern, eastern and south-western Australia since the 2016 state of the environment report is that they are generally in very poor condition with reduced ecological function. In northern Australia, they are generally in good condition and are able to maintain minimum expected function (with reduced function, or even persistent transformation, in some localised areas).

Aquatic ecosystems are recognised as being among the most vulnerable to climate change. They experience both local changes and the cumulative effects of changes in the surrounding landscape (see Cumulative pressures), as well as exposure to a wide range of extreme climatic events such as floods and droughts (see Extreme events).

Freshwater ecosystems are particularly vulnerable to pressures from climate change, which is predicted to cause substantial changes to the mix of species in Australian rivers well before the end of this century (James et al. 2017). Altered water quality and quantity, as a result of climate change and resource extraction, are having major detrimental effects on freshwater biodiversity. Extreme hot and dry weather events in the northern Murray–Darling Basin between 2017 and 2019 have been amplified by climate change. The combination of hot conditions, low flows and significant algal blooms during the 2018–20 major drought resulted in mass fish deaths in the Basin (Koehn et al. 2020b). In 2015, a new, unknown disease caused the near extinction of an Australian freshwater turtle, the Bellinger River snapping turtle (Myuchelys georgesi), as a result of deteriorating water quality and climate change (Spencer et al. 2018). Future changes in the global climate system are likely to have an even more profound impact on hydrology.

In other waterways, there is an increased risk of algal blooms. The 2019–20 drought and bushfires reduced vegetation cover, and increased the levels of dry soils and ash. This means that following rains could wash large amounts of sediments and nutrients such as phosphorus into waterways, triggering blooms. Algal blooms can produce toxins and reduce the oxygen content of water, affecting fish and other oxygen-dependent organisms (Productivity Commission 2021a).

Murray–Darling Basin

In the Murray–Darling Basin – home to 16 internationally significant Ramsar wetlands, 35 endangered species and 98 species of waterbirds – rivers and catchments are mostly in poor condition, and native fish populations have declined by more than 90% in the past 150 years: a trend that appears to be continuing today (Koehn et al. 2020b).

The drier conditions of a changing climate, coupled with constraints on environmental water management, have meant that the flooding of wetlands (particularly at Ramsar sites) has not met objectives even in wetter periods. For example, the extent, magnitude and duration of flooding of wetland woody vegetation communities is considered to be inadequate to meet their ecological requirements for the maintenance of extent and condition in most cases (Chen et al. 2020). Low-flow provisions in extreme conditions have not been adequate to protect critical environmental connectivity and refugia in many systems. Reduced water availability also affects water quality, which in turn degrades aquatic ecosystems and causes loss of habitat for flora and fauna, followed by a decline in populations (Productivity Commission 2021a).

The 2020 evaluation of the Murray–Darling Basin Plan found that its implementation over the previous 7 years was ‘having a significant and positive impact on the Basin environment’ (MDBA 2020). Others submit that these effects are highly localised and short term in nature, the amount of environmental water available is too little to have a sustained and widespread benefit (see also Environmental water), and there is little peer-reviewed evidence of systemic improvement of any flow-dependent matter of national environmental significance or any tributary river system (Wentworth Group of Concerned Scientists 2021).

Assessments of the state and trend of threatened species in the Basin are limited to flow-dependent fish and waterbirds, and tend to focus on particular species or regions. Recent assessments have shown positive outcomes for some threatened species (in some locations at some points in time), but monitoring and reporting on the state and trend of threatened species in the Basin are largely inadequate to assess whether the Basin Plan is achieving its environmental objectives (Ryan et al. 2021).

The Echuca Declaration 2007 reinforced the rights and aspirations of Indigenous people in water management, including the importance of cultural flows as water entitlements that are legally and beneficially owned by Indigenous communities. Indigenous people in the Murray–Darling Basin own 0.17% of water access entitlements and water licences, despite being nearly 10% of the population (Hartwig et al. 2020). The 2021 final report of the Cultural Water for Cultural Economies project states the clear message of Traditional Owners that water should not be traded or piped out of the Murray–Darling Basin river system, and water should be transferred to Indigenous people through a process determined and designed by them (O’Donnell et al. 2021) (see also Water resources).

Wetlands

Australia has nearly 34 million hectares of wetlands, covering 4.4% of the continent (Bino et al. 2016), half of which are floodplains and swamps. Australia has 66 Ramsar wetlands that cover more than 8.3 million hectares; Ramsar wetlands are those that are included on the List of Wetlands of International Importance held under the Ramsar Convention on Wetlands of International Importance Especially as Waterfowl Habitat. Wetlands provide important environmental, social, cultural and economic services. They are often significantly affected by changes in agricultural and urban landscapes through extensive clearing, introduction of non-native species, alteration to flows and concentrated grazing pressure. They are also vulnerable to further hydrological changes and drying under future climate change scenarios (Finlayson et al. 2017). Drought conditions, in conjunction with increased consumptive water use, result in a decrease in flows into wetlands and reduction in inundation. The 2019 Aerial Survey of Wetland Birds in Eastern Australia (Porter et al. 2019) found that the wetland area index was the lowest since surveys began in 1983.

Grazing, pests and weeds are also having a significant impact on wetland health, emphasising the need for integrated management of land-based pressures as well as inundation. For example, nest predation by invasive foxes has been implicated in declines in freshwater turtles in the Murray–Darling Basin (Van Dyke et al. 2019).

Several major indices for waterbirds continued to show significant decline as drought conditions and consumptive water use resulted in a decrease in flows into wetlands. The 2019 Aerial Survey of Wetland Birds in Eastern Australia (Porter et al. 2019) found that the wetland area index was the lowest since surveys began in 1983. Impacts were not confined to eastern Australia – on 30 June 2020, Lake Argyle in Western Australia, a listed Ramsar wetland, was at its lowest end-of-year level in almost 30 years (BOM 2021a).

Wetland ecosystems underpin all aspects of living Indigenous cultures, and hold significant ecological, recreational, spiritual, cultural and economic significance for Indigenous Australians. In some areas of central and northern Australia, wetlands and billabongs are particularly threatened by invasive feral hoofed animals, including water buffalo, pigs and cattle. For example, Indigenous knowledge holders tell us that, historically, yarlbun (water lily) grew in billabongs year‑round and was a staple part of people’s diets. However, since the introduction of hard-hoofed ungulates, and their subsequent proliferation and spread, there have been substantial declines in the yarlbun cover of billabongs in the late dry season when water resources become scarce, and animals concentrate around the persisting billabongs. Indigenous knowledge suggests that some billabongs have passed an eco-cultural threshold, shifting from a yarlbun-dominated system to a turbid, sediment-dominated system driven by feral animals (Ens et al. 2016, Russell et al. 2021).

Groundwater species

Although groundwater systems and their dependent ecosystems are generally slower to respond to climatic conditions, they are also under significant pressure from drought and prolonged dry periods. This is because lower rainfall means that groundwater levels are not replenished, and because extraction may increase when surface water resources are depleted. The lower-than-average groundwater levels experienced in 2018–19 in many parts of Australia persisted in 2019–20.

Many Australian ecosystems are dependent on groundwater, and all states and territories have recognised the need for common arrangements in managing significantly interconnected surface water and groundwater resources (Productivity Commission 2021a). Ecosystems that depend on groundwater include terrestrial ecosystems that access subsurface groundwater; the subterranean fauna of cave and aquifer systems; nearshore marine environments that receive groundwater discharges; and springs, wetlands and rivers that rely on groundwater for base flow, particularly in dry conditions. Examples of ecosystems in Australia that depend entirely on groundwater are the Great Artesian Basin spring ecosystems, the Pilbara spring ecosystems, and the permanent lakes and wetlands of the Swan Coastal Plain (Harrington & Cook 2014).

Groundwater access can also be pivotal in supporting urban ecosystem function in prolonged droughts, and in buffering the impacts of climate variability (Marchionni et al. 2020). Of ongoing concern is our lack of adequate knowledge of Australia’s diverse and unique subterranean aquatic fauna (stygofauna) that populate our underground water systems in very restricted ranges, particularly in relation to the assessment of impacts from large-scale developments.

Marine and coastal ecosystems

Australia’s rich marine ecosystems span from nearshore reefs to the soft-sediment communities of the abyssal plains at depths of more than 5,000 metres (m), encompassing the vast waters of open ocean that lie between the surface and the sea floor. Coastal ecosystems encompass dunes, saltmarsh, mangroves and estuaries that provide the essential connection between land and sea.

Marine habitats assessed in this report are currently in a range of conditions, from very good to very poor, and their trajectory ranges from stable to deteriorating. Coastal habitats and species were generally assessed as poor and deteriorating. Notably, Traditional Owners assessed marine habitats and communities as in worse condition than reflected by the western science assessments, although Indigenous assessments relate to different spatial scales (local, regional) that can be in a poorer state than the overall national scale.

Climate change continues to drive long-term shifts in the key physical characteristics of Australia’s marine and coastal zones, highlighted by recent record-breaking marine heatwaves (Santoso et al. 2017) and enduring changes in marine ecosystems documented over the past 5 years.

Australia’s marine waters are undergoing ‘tropicalisation’, as rising water temperatures drive warmer-water species to extend their ranges poleward into cooler temperate waters (see Range shifts and extensions). Both coral and rocky reefs have experienced changes in the composition of local reef fish communities in recent years and declines in the abundance of species on large scales (Stuart-Smith & Edgar 2021b). Temperate species declined at the warm edge of their distribution. Likewise, some coastal fish communities declined because of coral bleaching and cyclones in the tropics, and losses of canopy-forming kelps in some parts of the temperate zone (Richardson et al. 2018, Stuart-Smith et al. 2018, Stuart-Smith et al. 2021). Since 2003, at least 198 Australian marine species have undergone long-term shifts in their geographic distributions, and range shifts are becoming more frequent (Gervais et al. 2021, Gervais & Pecl 2021). Changes in some microbial assemblages of temperate waters have also been observed, favouring smaller phytoplankton (Brown & Bodrossy 2021); this shift could reduce food availability higher up the marine food chain.

Coral reefs

Coral reefs are immensely valuable marine ecosystems, acting as spawning and nursery grounds for many fish species; as magnets for tourism and recreation areas; and as buffer zones against high tides, rising sea levels and storms for coastal areas and communities. Coral reef ecosystems are generally in poor condition and deteriorating. Unprecedented marine heatwaves in 2016, 2017 and 2020 resulted in the first-ever consecutive years of coral bleaching and widespread coral losses, both within and beyond the Great Barrier Reef (Figure 5). Since 2016, coral cover has decreased across the northern Great Barrier Reef (Stuart-Smith et al. 2017, AIMS 2020), at some locations in the North-west Marine Region, and in the Coral Sea (Harrison et al. 2019). Reefs along Western Australia’s Pilbara coast experienced repeated heatwaves that resulted in extensive coral mortality (Babcock et al. 2020, Evans et al. 2020).

Tropical cyclones also had substantial, but localised, impacts on Ningaloo Reef in Western Australia and the reefs of Queensland’s Whitsunday Islands. However, most offshore (oceanic) reef systems are in good condition, with fewer signs of human impacts than inshore reef systems, but may become threatened by warmer waters (Edgar et al. 2014). Southern parts of the Great Barrier Reef and Coral Sea have experienced increases in coral cover following previous disturbances. This variability indicates the dynamic responses of reef communities to climate change–driven pressures. Deepwater corals and sponges (from 30 m to more than 150 m in depth) remain in good condition; however, trends are unclear because ocean warming is posing an increasing threat.

Australia’s extensive string of shallow coastal rocky reefs and kelp (algal) beds that characterise temperate waters are economically, socially and ecologically significant. These have also been affected by rising temperatures. Across Australia, marine heatwaves have led to the loss of species from affected areas; the loss of major habitat types, including corals (Hughes et al. 2018), algal forests, seagrasses and mangroves (Wernberg et al. 2016, Babcock et al. 2019a); and the closure of fisheries (Caputi et al. 2019). Waters of south-eastern and south-western Australia are hotspots, with rates of warming above the global average.

Overall, the condition of the 8,000 kilometres or so of rocky reefs that run (southwards) from Brisbane to Perth is poor and deteriorating (Stuart-Smith & Edgar 2021a). The pressures on these ecosystems include rising ocean temperatures and marine heatwaves, nutrient and pH variations associated with changing currents, overgrazing by sea urchins and other species – due to climate change–driven range shifts and the removal of predators through fishing – and declining water quality due to coastal run-off.

However, conditions vary across regions. Reefs in southern (remote) regions remain in generally good condition, but those in the east and around major cities are poor. Large canopy-forming seaweeds are dominant in many locations in south-western Australia, and western Victoria and Tasmania, but overgrazing by sea urchins has had major impacts on natural rocky reef habitats in New South Wales, and eastern Victoria and Tasmania (Crozier et al. 2007, Ling & Keane 2018, Glasby & Gibson 2020). Overall, the condition of algal habitat nationwide is good but deteriorating as a result of warming waters and the cascading impacts of fishing (Barrett et al. 2021).

Water column and seabed habitats

Water column habitats in the open ocean extend from the relatively shallow waters over the continental shelf (0–200 m) to the deep offshore abyssal zone at depths of more than 4,000 m. The levels of chlorophyll-a (representing an index of phytoplankton biomass), zooplankton biomass and fish larval abundance (Richardson et al. 2021a, Richardson et al. 2021c, Trebilco 2021) indicate that these habitats are currently healthy. However, the water column is vulnerable to climate change–driven acidification and declines in dissolved oxygen, as well as fishing and pollution.

Marine canyons and seamounts are key ecological features: canyons provide pathways for the transport of sediments and nutrients (and pollutants) from the continental shelf to the deep sea and, likewise, the upwelling of cold, nutrient-rich waters from the deep ocean towards the shelf (Kämpf 2010, Currie et al. 2012). The health of these ecosystems varies widely, from very good to very poor, depending on historical levels of damaging bottom fishing and slow recovery rates (Althaus & Williams 2021, Nichol et al. 2021). Ocean acidification linked to climate change is an emerging threat (see Other climate-related changes), particularly for vulnerable corals and other calcifying organisms, as is pollution.

Other seabed habitats and communities include those found on silt, sand and gravel sea floors at all depths, as well as reef habitats and communities deeper than 30 m in both temperate and tropical waters. These include ‘twilight’ reefs (30–150 m depth, where small amounts of light still penetrate) and ‘dark’ reefs (below 150 m) formed by deepwater corals (both hard and soft corals), sponges and bryozoans. These habitats are generally in good condition, but again conditions are highly variable across and within regions, largely linked to historical and current commercial bottom fishing (Pitcher 2016, Pitcher et al. 2018). As there is little monitoring of the deep sea floor in Australia (apart from subsea pipelines), biodiversity or oceanographic trends are unknown, as are the impacts of plastics, dissolved pollutants and underwater cables.

Coastal habitats

Along Australia’s coasts, mangroves, saltmarshes, seagrasses, algal mats and native terrestrial vegetation provide habitat for numerous species; their health and extent are important for their own and other species’ survival. Saltmarshes are also efficient carbon sinks, storing an estimated 200 million tonnes of organic carbon (Macreadie et al. 2017). Australia-wide, 47–78% of saltmarshes and mangroves have been lost since European settlement, and they continue to deteriorate (Serrano et al. 2019).

Although mangroves have occupied Australian shorelines for more than 50 million years, and are increasing their range and cover in many areas, the past 5 years have demonstrated that they are not immune to the impacts of extreme events. Cumulative impacts, such as marine heatwaves, severe drought and a temporary drop in sea level due to a strong El Niño event (Duke et al. 2017), have been linked to massive mangrove dieback in northern Australia.

Many species of grasses, herbs, rushes, sedges and shrubs are found in Australian saltmarshes, mostly growing between mean sea level and the inundation limits of the highest tides. These have experienced losses over the past 5 years. Recent southwards encroachment of mangroves, due to warming temperatures, has driven the ongoing decline of saltmarshes. Flood control measures installed in eastern Australian estuaries from the 1950s to the 1970s isolated mangroves and saltmarshes from tidal waters, with a loss of some 65,000 hectares of saltmarshes in New South Wales and 35,000 hectares in Queensland (Rogers et al. 2016, Wegscheidl et al. 2017). In more recent years, the expansion of solar salt fields in north-west Western Australia has also impacted areas of mangrove and associated algal mats, and saltmarsh communities. The Western Australian Environmental Protection Authority has determined that consideration of any new developments should be in the context of the reasonably foreseeable impacts from all proposals and past developments. Understanding the cumulative impacts from existing and new proposed operations will be critical to minimising the overall impacts.

Australia boasts about 40% of the world’s seagrass species, which form meadows on intertidal and subtidal sediments around Australia. These include several species only found in Australia, and some of the world’s largest meadows. Seagrasses form the base of the food web; stabilise sediments; provide vital nursery habitat for important commercial, cultural and recreational fisheries (Unsworth & Cullen-Unsworth 2014); and are a globally significant reservoir of carbon (Serrano et al. 2019). Historical seagrass losses are extensive (20–26% loss since European arrival) (Waycott et al. 2009) and ongoing. Although healthy seagrasses largely remain in low-population areas, combined pressures from water quality changes, climate change, weather extremes and the movement of species into new areas have seen declines in seagrass in developed areas. Although there have been some areas of seagrass recovery in the past 5 years (e.g. in some parts of the Great Barrier Reef region), both the general extent and the condition of seagrasses remain poor relative to historical records.