Biodiversity: Habitat-forming species



Saltmarshes and mangroves (see Mangroves) are the dominant biological wetland types of the upper intertidal zone along the Australian coastline. Saltmarshes play a vital role in sequestering carbon, and function as habitat and nursery sites for diverse faunal communities, including birds, fish and insects (Laegdsgaard 2006). They are, however, among the most neglected type of wetland in Australia (Boon 2012), and are listed as a threatened ecological community under the New South Wales Threatened Species Conservation Act 1995 and the EPBC Act.

The position of saltmarshes high on the shoreline and their arguably displeasing aesthetic has led to extensive historical losses and a suite of present-day pressures (Saintilan & Rogers 2013). At local or regional scales, total loss of saltmarsh has exceeded 50 per cent in some areas. For example, it is estimated that Sydney Harbour has lost 85 per cent of its original saltmarsh habitat (Mayer-Pinto et al. 2015). Tropical saltmarshes are extensive, but are much less studied.

The threats to saltmarshes are diverse and variable in spatial scale. There is a widespread issue of mangrove encroachment (Saintilan et al. 2014), where the expansion of mangroves squeezes saltmarshes into landward barriers. Invasive species are a problem in south-eastern Australia (Hurst & Boon 2016), and include common cordgrass (Spartina anglica), groundsel bush (Baccharis halimifolia), pampas grass (Cortaderia selloana) and spiny rush (Juncus acutus). There is a historical legacy of pollution in sediments that, if disturbed, has the potential for broad impacts. Oil spills are an unpredictable threat; however, few have occurred in Australia and considerable contingency plans are in place.

A major threat to saltmarshes is clearing and drainage for mosquito control (Dale & Hulsman 1990). Saltmarshes are becoming increasingly fragmented, causing decreased biodiversity, resilience, sediment trapping and nutrient cycling; and altered food-web dynamics. Permitted and unpermitted tourist and recreational use, such as damaging 4WD activity or storage of tenders to access yachts, occurs in some locations. Other threats include tidal restriction, dredging, draining, eutrophication, acid sulfate soils, water pollution, saltwater inundation, grazing and erosion. In the future, climate change impacts are expected from sea level rise, rising carbon dioxide levels and temperature, increased frequency of extreme events, and acidification of floodwaters. Climate change processes may exacerbate to a ‘coastal squeeze’ on saltmarshes caught between land-based and sea-based pressures.

Historically, saltmarshes have been lost to land reclamation (including draining) and more recently to mangrove encroachment in New South Wales, Victoria, South Australia, southern Queensland and Western Australia. Approximately a decade ago, Victoria had approximately 192 square kilometres of saltmarsh and 32 square kilometres of estuarine wetland (Boon et al. 2011), but this is now greatly reduced. In South Australia, mapping in 2000 indicated that approximately 3.3 per cent of intertidal and 4.7 per cent of supratidal saltmarshes were degraded or displaying dieback; these proportions are likely to have remained largely unchanged, with losses occurring predominantly near urban centres.

Recent closure of salt fields north of Adelaide has provided an opportunity for saltmarsh restoration. However, 2 species of introduced seablite (Suaeda baccifera and S. aegyptiaca) are present and likely spreading in South Australia. Invasion of cordgrass (Spartina spp.) is also an increasing threat in Tasmania and Victoria, although management strategies are successfully implemented in Tasmania. In Queensland and Western Australia, salt production is a past and present cause of saltmarsh loss, but in the tropical north, development pressure is low and there are extensive saltmarsh and salt pan areas.

Saltmarshes are high-risk coastal habitats and current management is insufficient (Rogers et al. 2016). Currently, saltmarsh management is largely a local- and state-run operation, and variation between states in approaches can make it difficult to compare programs in terms of success and effectiveness. Development of recovery plans requires greater understanding of species of high functional importance, responses of saltmarshes to the plethora of threats, regulating factors such as nutrient inputs and herbivory, ecosystem function and services, and hydrology (relationship with tide, groundwater and fresh water; see Box COA8). Furthermore, recovery requires increased public recognition of the value of saltmarshes, and policy change to allow inland saltmarsh to respond to rising sea levels. Understanding of saltmarsh regeneration is still in its infancy, although early indications are of long restoration times and potential for mangrove encroachment into restored areas.

The short-term outlook for temperate saltmarshes has improved because of state and national conservation and planning in the past decade, along with growing public awareness. However, the longer-term outlook for temperate saltmarshes is poor, especially where site geology (e.g. incised valleys) or coastal development limits opportunities for inland retreat to accommodate rising sea levels and mangrove encroachment. The long-term outlook for tropical saltmarshes, where development is lower, is one of greater opportunity for inland retreat.

Box COA8 Saltmarsh restoration

The Mungalla wetlands east of Ingham, on the north Queensland coast, are typical of many tropical coastal wetlands that flow into the Great Barrier Reef lagoon. Historically, they have been used for many thousands of years by Indigenous Australians to provide food and fibre, and were sustainably managed by them for their spiritual and ecological values. The ecological functions of this important coastal zone include an interconnected habitat complex of tidal and freshwater wetlands, which provides critical nursery and feeding services for a range of aquatic and land flora and fauna.

The introduction of western agriculture to the Great Barrier Reef catchment around 100 years ago has led to the progressive loss and degradation of coastal wetlands through a combination of earth bunding (where retaining walls are used to keep water back) to reclaim land for pasture, and upstream agricultural use (grazing and sugar cane production), which leached ecologically damaging nutrients and sediments. As a result, most of the coastal wetlands (40–90 per cent) were lost, and those that remained were highly infested with weeds. This was the situation with the Mungalla coastal wetlands until the property was acquired in 1999 by the Nywaigi Aboriginal Land Corporation, providing an opportunity for Nywaigi people to re-establish links with their Country and introduce their own form of land and wetland management. This began in 2001, after the formation of the Mungalla Aboriginal Corporation for Business (MACB), which operates a cattle-grazing enterprise, with a combination of agisted and owned stock. MACB also entered a partnership with scientific advisers from CSIRO and Tropical Water and Aquatic Ecosystem Research, James Cook University, to monitor and restore the ecology of the Mungalla wetlands within the property.

Ecological conditions were extremely poor during the first decade, with massive weed infestations causing very low dissolved oxygen conditions that greatly degraded the wetland biodiversity. Initial attempts at weed control using chemical herbicides were expensive, ecologically undesirable and of limited success. Eventually, it was decided to investigate a more natural form of weed control using tidal ingress of seawater by removing an earth bund on the seaward side of the wetland. To give some confidence that this might work, CSIRO first carried out some simulation studies using sophisticated hydrodynamic modelling, which showed that, during large tides, sea water should penetrate well into the wetland.

The earth bund was removed at the beginning of October 2013, and subsequent monitoring of the depth and salinity in the wetland showed that sea water did indeed enter the wetland several times a year on the highest tides. The ecological response was remarkable, as the freshwater weeds were immediately reduced and became almost entirely absent within 2 years of removing the bund. Specifically, there was a 39 per cent decrease in olive hymenachne (Hymenachne amplexicaulis), a 76 per cent decrease in water hyacinth (Eichhornia crassipes) and a 37 per cent decrease in salvinia (Salvinia molesta). Two years following the bund removal, saltmarsh communities such as native sedges, primarily bulkuru (Eleocharis dulcis), dominated the site. Wetland biodiversity has greatly improved, with more aquatic species and increased bird numbers. The greatest reward for this approach is that it is ecologically sound and the tidal ingress will continue, cost free.

The other key lesson from the successful restoration of the Mungalla wetlands is that it relied on the combination of Indigenous ownership and management with scientific monitoring and modelling—an approach that could well be applied to many of the currently degraded coastal wetlands in northern Queensland.

Photos taken 50 metres above the bund wall that show the massive infestation of Weeds of National Significance, before the bund was removed (October 2012), and the enormous reduction in these weeds only 2 years after the bund was removed (October 2014)

Photos taken 50 metres above the bund wall that show the massive infestation of Weeds of National Significance, particularly water hyacinth, before the bund was removed (October 2012), and the enormous reduction in these weeds only 2 years after the bund was removed (October 2014)

Photos taken in October 2012, 50 metres above the bund wall, that show the massive infestation of Weeds of National Significance, particularly water hyacinth, before the bund was removed  and the reduction in these weeds only 2 years after the bund was removed (October 2014)

Photos taken in October 2012, 50 metres above the bund wall, that show the massive infestation of Weeds of National Significance, particularly water hyacinth, before the bund was removed  and the reduction in these weeds only 2 years after the bund was removed (October 2014)

Two years following the bund removal, saltmarsh communities such as these native sedges, primarily bulkuru (Eleocharis dulcis), dominate the site

Two years following the bund removal, saltmarsh communities such as these native sedges, primarily bulkuru (Eleocharis dulcis), dominate the site

Two years following the bund removal, saltmarsh communities such as these native sedges, primarily bulkuru (Eleocharis dulcis), dominate the site

Photo by Carla Wegscheidl

Source: Jim Wallace and Ian McLeod, James Cook University


Australia is home to a diverse suite of mangrove species, including 1 endemic species, Avicennia integra. Mangroves are broadly distributed around the Australian coastline, excluding Tasmania. Mangroves form structurally complex and productive habitats that serve as critical nursery grounds for fish; habitat for sediment infauna; and habitat for a wide range of species that frequently use mangrove resources, including birds, terrestrial vertebrates and, in the north, crocodiles. Nationally, most mangroves occur in remote areas free of significant human development; however, in 2015–16, there was a large-scale dieback of mangroves in the Gulf of Carpentaria (around 10 per cent of Australia’s cover) and other locations (e.g. Mangrove Bay, Ningaloo Marine Park, Western Australia), associated with prolonged drought.

Generally, a low proportion of mangrove species throughout Australia are threatened (Polidoro et al. 2010). Increasing growth and extent of mangroves in south-eastern Australia is attributed to favourable anthropogenic conditions, such as higher nutrients, sedimentation, sea level rise, atmospheric carbon dioxide and coastal development (Saintilan et al. 2014). Trends in the north of Australia are less predictable, with some locations experiencing increased extent, and others shrinking because of erosion (Asbridge et al. 2016).

Reforms in the 1970s and 1980s largely prevented further mangrove decline caused by development (Rogers et al. 2016). However, in some locations, particularly near developed areas, mangroves are severely affected by several pressures, including modified hydrology, exposure, burial, erosion, pollutants, clearing, land-use change, and limited potential for retreat in the face of rising sea levels.

In Victoria, mangroves cover approximately 52 square kilometres (Boon et al. 2011) and are in generally good condition. Mangroves remain pressured by local coastal developments, because they are not protected in Victoria beyond the approval pathways of relevant planning schemes or by the Coastal Management Act 1995. Mangroves in Queensland are facing direct and indirect threats, including agricultural run-off (e.g. locations in Torres Strait), intense cyclones, erosion, flooding and drought. Mangroves in Western Australia are subjected to cyclones and sea level rise (Lovelock et al. 2015), although there is no large-scale evidence of reduced quality. Pollution and erosion have contributed to the degradation in some South Australian mangrove habitats, which are also vulnerable to sea level rise, and degradation in Darwin Harbour is linked to pollution and development pressures.

There is information on the extent of mangroves, but a lack of monitoring and evaluation of their function, productivity and condition. There is a pressing need to quantify carbon sequestration dynamics of mangroves (and saltmarshes) throughout Australia. State-level assessments are sometimes better, although they lack uniform methods and comparability, particularly for temporal trends. Further, few state or national mitigation or rehabilitation strategies exist. However, one example of implemented strategies is the successful restoration of mangrove habitat in some sections of the Hunter River, New South Wales.

The outlook for mangroves in the short term is good, as they are widely protected and are generally not cleared. In the longer term, mangroves are threatened by climate change and other anthropogenic pressures, but are well positioned to deal with these threats. Mangroves in north-western Australia are predicted to decline in response to changing salinity regimes associated with drought, but increase southwards in southern Australia because of increasing temperatures and atmospheric carbon dioxide (Alongi 2015). Predicted climate change–driven alteration of rainfall patterns around the nation is likely to alter mangrove productivity and growth, which decreases with lowered rainfall. In southern Australia, mangroves are threatened by coastal development, a process sometimes aided by public dislike for various features, including the aesthetics, of this habitat.


Seagrasses are flowering plants that form meadows on intertidal and subtidal sandy and muddy sediments around Australia. The condition of seagrass meadows can be assessed by quantifying the area of cover, density, biomass and species composition, or measures of resilience such as genetic diversity, seed reserves and flowering frequency. Seagrasses play a vital role in carbon cycling (Forqurean et al. 2012), primary production and sediment stability, and provide habitat for a diverse range of fauna. Historical seagrass losses are extensive, and recovery times can range from months to centuries depending on the species. It is likely that seagrass is in poor condition in more locations than are currently known (Waycott et al. 2009). Some populations are stable or have increased in cover, particularly in areas away from human habitation, where water quality has improved or where land reclamation rates have decreased.

Seagrass is threatened by numerous processes, including nutrient input and eutrophication, herbicides, toxicants, disease, reduced light, increased sedimentation loads and resuspension, dredging, algal blooms, boating (anchoring and mooring), and habitat loss to flooding and coastal development. Climate change and associated increases in extreme weather events are a long-term threat to these critical habitat-forming species (Short & Wyllie-Echeverria 1996).

In the north, seagrass habitat in Torres Strait appears to be in good condition. There are little data for the far northern Great Barrier Reef or the Gulf of Carpentaria, but these regions are likely to be in good to very good condition. In the Great Barrier Reef, monitoring of about 45 inshore seagrass meadows indicates that their overall abundance has declined along the northern, central and southern coasts (McKenzie et al. 2015b). Other indicators of the condition of seagrass meadows, such as reproductive effort and nutrient status, have also deteriorated (McKenzie et al. 2015b). These declines are a consequence of multiple years of above average rainfall, poor water quality, and climate-related impacts followed by extreme weather events (tropical cyclones Larry and Yasi) in early 2011 (GBRMPA 2014). Populations on the east coast of Queensland are recovering, but remain in a vulnerable condition (McKenzie et al. 2015b). Other examples of declining intertidal and subtidal meadows include Mourilyan Harbour, where seagrass meadows had been consistently present since 1993, but are now in very poor condition (Reason et al. 2016), as well as substantial reductions in the meadows adjacent to Cairns (McKenna et al. 2015), Townsville (Davies et al. 2013, McKenzie et al. 2015a) and Gladstone (Sankey & Rasheed 2011, Carter et al. 2015), although the meadows are recovering.

In New South Wales, some populations of the seagrass Posidonia australis are recognised as threatened communities. The condition of seagrass in Victoria is good near Melbourne and eastwards. In South Australia, recent losses have been observed at Kangaroo Island, whereas other areas (e.g. around Adelaide) have not fully recovered from historical losses. The relatively unmodified northern and western coasts of Australia likely support large areas of pristine seagrass habitat. In Western Australia, seagrass is in very good condition in the northern regions, such as the Kimberley, and some southern areas, such as Geographe Bay. However, seagrass is in poor condition in some southern parts of Western Australia, such as Cockburn Sound, Perth and Leschenault Inlet, and the more northern Shark Bay. Relatively little is known about seagrass populations in the Northern Territory.

Pressures on seagrass are set to continue in the short term, particularly near centres of coastal development (Waycott et al. 2009). Trends in seagrass decline could be minimised by appropriate management, the prospect of which improves when seagrasses are recognised as high-priority species for conservation. To achieve effective management of seagrasses, we must improve our understanding of not only their extent and distribution, but also the spatial and temporal distribution of pressures, impacts and seagrass tolerance to environmental change (Kilminster et al. 2015). The long-term outlook is uncertain, and will depend on how species can respond to changes in water temperature, sea level, storm activity, freshwater inputs and erosion.

Clark GF, Johnston EL (2016). Coasts: Biodiversity: Habitat-forming species. In: Australia state of the environment 2016, Australian Government Department of the Environment and Energy, Canberra,, DOI 10.4226/94/58b659bdc758b