Ecological processes and species populations


Assessing water-related ecological processes and species populations further indicates the health of aquatic ecosystems. Processes and populations add a layer of assessment that integrates many of the individual parameters assessed in previous sections.

State and trends of ecological processes

Broadscale health assessment for aquatic ecological processes relies on a background of compliance monitoring, overlaid by programs at the level of individual regions, initiatives or issues. Reporting across the country varies in scale, scope, timing and nature, although standard or common methodologies—such as the Australian River Assessment System and stream condition indices—assist in collating and comparing assessments. Several new and updated assessments have been released since 2011, providing support for this report.

Bunn et al. (2014) produced a landmark assessment of the ecological responses to altered flow regimes for the Murray–Darling Basin, based on 5 research questions:

  1. What are the different types of freshwater ecosystems and where are they?
  2. What are the flow-related threats to freshwater ecosystems, and how do they differ across the Murray–Darling Basin?
  3. How do freshwater ecosystems respond to these flow-related threats, and what is the likelihood they will respond to environmental flows?
  4. Can river managers optimise the delivery of environmental flows to improve environmental outcomes?
  5. How can river managers measure the success of the application of environmental flows?

A Basin-scale classification of freshwater ecosystems was developed to help address these questions. This classification was used to assess how ecosystems were affected by threats such as water resource development and land-use change. Impacts were found to vary across the Basin—some freshwater ecosystems were affected more by water resource development than others, whereas the cumulative effect of bores, farm dams and levees posed a greater threat to freshwater ecosystems than that posed by large dams in some regions. The assessment demonstrated that provision of environmental flows can, to some extent, be used to address ecosystem degradation, and an approach was developed to improve the environmental benefit of flows released from environmental water holdings.

Another recent formalised approach for assessing ecological responses to altered flow regimes is the ‘eco evidence’ method of Webb et al. (2013). Their analyses found strong support for many hypotheses regarding ecological impacts, with a consistent sensitivity to changes in flow regime for fish and riparian vegetation across a variety of performance metrics. Macroinvertebrate responses were more varied, although largely consistent with these performance metrics. The ecology associated with different flow regimes has also been investigated in Tasmania (Warfe et al. 2014), and Bice et al. (2014) further investigated responses of a range of small-bodied and large-bodied Murray River riverine fish species, highlighting the species-specific responses that occur with different components of a managed flow regime. Other recent flow–ecology investigations have considered fish (Vilizzi et al. 2014, Wedderburn et al. 2014, Rayner et al. 2015), macroinvertebrates (Chessman 2015), vegetation (Campbell et al. 2014), and carbon and energy (Cook et al. 2015). Ecological and water quality responses of floodplains and wetlands have also received attention (Beesley et al. 2012, Jardine et al. 2012, Pettit et al. 2012).

The South Australian NRM report cards indicate that aquatic ecological condition is assessed as good to fair in the north-east of the state (in the Lake Eyre Basin division), and fair to poor in the south-east. Aquatic ecological condition is reported as unknown across the west of the state, in the South Western Plateau division, and no trend information is available.

In addition to analysis of future risks from development and climate change, the Northern Australia Water Futures Assessment (Close et al. 2012) characterised surface-water and groundwater regimes, and ecological processes for northern Australia. Overall, the northern Australian catchments were reported to have a relatively low level of disturbance, with catchments such as the Mitchell and Gilbert in good ecological health. It was noted, however, that for regions in northern Australia there is a general lack of quantitative information on relationships between flow, and floral and faunal responses.

In Tasmania, the upper Tamar Estuary was assessed in 2015 as being in poor health, partly because of urbanised catchments, and poor-quality agricultural, stormwater and wastewater treatment plant run-off. Elsewhere, Hydro Tasmania reported that its monitoring of Woods Lake detected eggs and mature adults of the Arthurs paragalaxias fish (Paragalaxias mesote), previously thought to be locally extinct. Rehabilitation of the Lagoon of Islands achieved success, with zero toxic algal blooms, development of a diverse algal community and wetland vegetation recolonisation.

The condition of Victoria’s aquatic ecosystems, reported in 2013, was largely based on assessments made before 2011. Planned dates for the next group of assessments of Victorian wetlands, streams, estuaries and rivers are likely to be known in late 2016. The Living Murray’s 2013–14 assessment of icon sites, which range from the Barmah–Millewa Forest to the Murray Mouth, showed that ecological conditions had either improved or remained stable, benefiting from both natural floods and environmental watering. Future condition assessments will be available as part of monitoring of implementation of the Basin Plan’s Environmental Watering Strategy. The results of the first year of the Commonwealth Environmental Water Office’s Long-Term Intervention Monitoring Project show ecological benefits for stream metabolism, macroinvertebrates, vegetation, frogs and fish that generally range from probable to strong, with a small number of negative responses such as reduction in slack water area.

The 2015 New South Wales SoE report describes the overall condition of rivers across New South Wales as moderate, and gives the same rating for the condition and extent of wetlands. Coastal rivers in the South East Coast (New South Wales) division are in better ecological health than those of the Murray–Darling and Lake Eyre basins, whereas fish communities are in poor condition across the state, with continuing declines in the Murray–Darling Basin. Wetland condition is noted as having improved in areas benefiting from environmental watering, which has helped to maintain waterbird diversity. As an example at a local catchment scale, the Clarence catchment was reported in 2013 as having ecosystem health across subcatchments ranging from very poor to good, with a majority in fair condition, leading to an overall fair rating.

The Fitzroy Basin (Queensland) is the largest catchment delivering outflows to the Great Barrier Reef. Overall freshwater ecosystem condition reported across the basin for 2013–14 ranged from fair to good (Queensland Government 2015). Within this, ecological condition assessment included consideration of macroinvertebrates, PET (Plecoptera, Ephemeroptera, Trichoptera), taxa richness, SIGNAL (Stream Invertebrate Grade Number—Average Level) index and the percentage of tolerant taxa. Ecological condition assessments were only available for the Mackenzie, Theresa and Upper Isaac catchments, with most identified as having poor condition.

The South-East Queensland Healthy Waterways Partnership similarly reported most catchments to have poor to fair environmental condition, where poor indicates that many key ecological processes are not functional and most critical habitats are affected. No catchments were given a ‘fail’ grade, and Noosa—at the extreme north of the region—was rated as having an excellent environmental condition.

Queensland’s Q-catchments condition reports of 2012 included coverage of the Bulloo (Negus et al. 2013a), Nebine (Negus et al. 2013b), Paroo (Negus et al. 2013c) and Warrego (Negus et al. 2013d) catchments. The overall condition of riverine ecosystems in the Bulloo catchment was assessed as ‘slightly disturbed’, whereas the condition of the other 3 catchments was assessed as ‘moderately disturbed’.

Box WAT4 describes the success of a wetlands management program in Queensland.

The South West Index of River Condition (SWIRC) has been used to assess river condition across a range of areas in southern Western Australia, with most assessments for periods leading up to 2011. A 2015 assessment of the river health of the lower Blackwood reported that, overall, ‘the ecological health of the waterways was good, with most SWIRC theme scores for each system categorised as largely unmodified and slightly modified’ (White et al. 2015). The assessment was based on short-term monitoring, precluding commentary on trends.

The Biodiversity report provides further and broader information on the state and trends of species and ecosystems.

State and trends of key species populations


The 2014 aerial survey of waterbirds in eastern Australia (Porter et al. 2014) noted mostly dry wetland conditions across much of the survey area, reflecting a long period of below average rainfall. Trend analysis indicated a continuation of long-term declines in abundance, wetland area and breeding species richness. Environmental flows in areas such as the Macquarie Marshes were noted as delivering wetland benefits, albeit on scales much smaller than in years with above average rainfall. Overall, given the general drying conditions, waterbirds were concentrated in a small number of important sites. Lowest-on-record values of total breeding index and breeding species richness (Figure WAT16) were recorded, reflecting both the poor and declining state of waterbird populations across the region. The most recent aerial survey of waterbirds for the whole of Australia was completed in 2008, as part of the national waterbird survey led by the University of New South Wales.


Frog numbers in Australia continue to decline, in line with international trends, with significant threats arising from disease (e.g. chytridiomycosis) and loss of habitat. Since 2011, 3 species of frog have been added as critically endangered to the list of threatened species under the Environment Protection and Biodiversity Conservation Act 1999. The iconic southern (Pseudophryne corroboree) and northern (P.pengilleyi) corroboree frogs are under threat, with status either critically endangered or endangered at various administrative levels. Surveys of known sites for these frogs suggest that they are very close to extinction in the wild. A January 2014 survey of southern corroboree frog sites found only 6 males, with no eggs in their nests. Results are similar for northern corroboree frogs, although good population numbers have been observed in the Fiery Range area of New South Wales. Chytridiomycosis is also known to be present in South Australia, although the extent and effects on frogs are unknown.

Environmental watering has been used to some benefit for frog populations. Under The Living Murray program, environmental flows were found to provide benefits to frog populations in the Chowilla Floodplain, including a significant breeding response by southern bell frogs (Litoria ranifomis). Similarly, the Long-Term Intervention Monitoring Project recorded benefits of environmental watering for frogs in the Warrego–Darling (Commonwealth Environmental Water Office 2014) and Murrumbidgee (Commonwealth Environmental Water Office 2016) regions.


The 2013–14 Lake Eyre Basin assessment of fish populations reported that fish species richness for the major river systems varied from 3 species in the Macumba River to 18 species in Cooper Creek. Total abundance of fish was 4–5 times greater than in previous years, largely because of high catches of Lake Eyre hardyhead (Craterocephalus eyresii) in the lower Cooper and Diamantina catchments. Exotic species accounted for less than 1 per cent of the total catch, with the Neales catchment having the highest proportion of exotic species. No exotics were caught in the Finke, Macumba and Georgina catchments (Mathwin et al. 2015).

In Western Australia, the 2014 values of the Fish Community Index showed that fish communities in the Swan and Canning rivers had improved since the mid-2000s, although the 2014 values were consistent with the pattern of good to fair condition assessments in recent years, indicating a stable trend. The results indicate high and stable salinity in the Swan and Canning rivers, along with higher oxygen levels and an absence of significant toxic algal blooms. The Western Australian Government’s strategic assessment of Perth and the Peel region, a draft of which went to public consultation from December 2015 to May 2016, may provide a platform for future ecological improvements in the region.

For Murray–Darling icon sites, the Living Murray results from 2013–14 and previous years reflect recovery of fish populations after a significant blackwater event in 2011.


Little is known at a national level about state and trends in stygofauna since 2011. Stygofauna have been noted as being of relevance to the Bioregional Assessment Programme, with the Independent Expert Scientific Committee’s methodology noting that stygofauna ‘are recognised as a factor for environmental consideration under the Queensland Environmental Protection Act 1994; are valued as indicators of ancient aquifers and their water quality by the Western Australian Department of the Environment and Conservation; and are being actively researched in South Australia, New South Wales and the Northern Territory’ (Barrett et al. 2013). Active research is also under way in Western Australia (A Pinder, Western Australian Department of Parks and Wildlife, pers. comm., 7 July 2016).

Argent RM (2016). Inland water: Ecological processes and species populations. In: Australia state of the environment 2016, Australian Government Department of the Environment and Energy, Canberra,, DOI 10.4226/94/58b656cfc28d1