Aquatic species and communities Classification of aquatic habitats

The aquatic habitats in the Galilee subregion can be classified using the work of Jaensch (1999), Eamus et al. (2006), Kennard et al. (2010) and Fensham et al. (2011). None of these four classifications alone describes the range of water-dependent ecosystems at a consistent resolution sufficient for the BA methodology (Barrett et al., 2013), but in combination they provide robust coverage of the range of water-dependent ecosystem types.

Jaensch (1999) developed a classification of the wetlands of the south-western quadrant of Queensland, which included most of the Galilee subregion and all of the Lake Eyre Basin drainages as far as the South Australian border (Table 12). Fifteen of the wetland classes occur within the Galilee subregion and the remaining six occur nearby in the river basins that drain south-west from the subregion.

Table 12 Wetland types of south-western Queensland, as defined by Jaensch (1999)

Wetland type

Presence in subregion: Yes = present Near = present in Lake Eyre Basin, to the west or south

Waterholes and watercourses


Permanent river reaches and waterholes



Wooded watercourses



Shrubby floodplain watercourses



Watercourses without trees and shrubs


Freshwater lakes


Permanent, isolated freshwater lakes



Oxbows (cut-off river bends)



Temporary freshwater lakes without grassland



Temporary freshwater lakes with couch grassland


Saline lakes


Semi-permanent saline lakes



Temporary saline lakes




Gibber and interdunal claypan aggregations



Isolated claypans and canegrass swamps



Sedge swamps



Forb meadows on floodplains



Lignum swamps



Bluebush swamps



Cooba shrubby swamps



Eucalypt wooded swamps



Acacia/belah wooded swamps




Artesian springs




Rockholes in arid upland


Eamus et al. (2006) proposed three simple primary classes of groundwater-dependent ecosystems:

  • ecosystems dependent on the surface expression of groundwater, including baseflow rivers and streams, wetlands, some floodplains and mound springs. This class of groundwater-dependent ecosystems requires a surface expression of groundwater, which may, in many cases, then soak below the soil surface and thereby become available to plant roots
  • ecosystems dependent on the subsurface presence of groundwater, often accessed via the capillary fringe (non-saturated zone above the saturated zone of the watertable) when roots penetrate this zone. No surface expression of groundwater is required in this class of groundwater-dependent ecosystems. In this product, this class (specifically the Coolibah – Black Box Woodlands) has already been discussed in Section, and will not be considered further
  • aquifer and cave ecosystems. These ecosystems include karstic, fractured rock and alluvial aquifers. The hyporheic zones of rivers and floodplains is considered in this category because these ecotones often support species that are obligate groundwater inhabitants.

Through an analysis of stream gauge data from across Australia, Kennard et al. (2010) developed a classification of surface water flow regimes for creeks, rivers and river segments. Four of twelve flow regime classes occur in watercourses in the Galilee subregion:

  • unpredictable intermittent
  • predictable summer highly intermittent
  • unpredictable summer intermittent
  • variable summer intermittent.

Within the bounds of the subregion, the ‘unpredictable intermittent’ flow regime class was only identified in the upper parts of the Flinders river basin, the northern-most river basin. Each of the other three flow regime classes was found at least once in most of the other seven river basins represented in the subregion. Where data were available for more than one stream gauge along a single river or creek, different stretches were assigned to different flow regime classes, indicative of systematic longitudinal variation of flow patterns or analytical difficulty leading to somewhat similar flow patterns being assigned to different regime classes. Although with different seasonality and predictability, all observed river flow regimes are intermittent, meaning that the rivers largely dry up and retreat to waterholes between major flow events (Kennard et al., 2010).

Fensham et al. (2011) developed a classification of permanent water bodies and natural wetlands, along rivers and elsewhere, for an area that substantially overlaps the subregion:

  • waterholes – enlarged segments of an ephemeral or seasonal river or watercourse which hold water after streamflow has ceased
  • rockholes – natural hollows in rocky landscapes, formed from fracturing and weathering, which store water from local runoff
  • outcrop springs (referred to as recharge springs in the earlier terminology of Fensham and Fairfax (2003)) – dependent on groundwater and occurring where sediments that form the aquifer are outcropping
  • discharge springs – dependent on groundwater that emanates through confining beds (aquitards) in areas remote from where the aquifer receives its inputs.

The three classifications described above, while individually incomplete, can be combined to form a classification with 11 possible classes as the basis of analysing aquatic ecology in water bodies in the Galilee subregion:

  • permanent lakes (both saline and semi-saline)
  • impermanent lakes (both saline and semi-saline)
  • permanent waterholes
  • impermanent waterholes
  • swamps
  • permanent rockholes
  • impermanent rockholes
  • permanent outcrop springs
  • impermanent outcrop springs
  • discharge springs (always permanent in the subregion)
  • subsurface water bodies or aquifers. Diversity and ecological drivers in aquatic habitats

There is a growing, but not yet comprehensive, literature on the key ecological drivers of aquatic communities of the Galilee subregion from which important principles are summarised in this section.


Silcock (2009) identified four permanent to semi-permanent major lakes in the Galilee subregion: Lake Galilee (almost permanent), lakes Dunn and Huffer (semi-permanent), and Lake Buchanan (highly dynamic, and usually dry by the middle of each dry season). All are located in the Desert Uplands IBRA bioregion in the centre and east of the Galilee subregion. All are semi-saline playas fringed by one or more classes of swamp in the sense of Jaensch (1999), especially samphire associations and Eucalypt wooded swamp or Acacia/belah wooded swamp (Caring for Our Country, 2012a, 2012b). While these lakes are known as important habitat for waterbirds, including some EPBC-listed species, the lakes’ ecology is not well studied.

There are numerous small, infrequently filled playas in the central Galilee subregion. In addition, the rivers draining from the Galilee to the south and west (the Diamantina, Cooper, Bulloo, Paroo and Warrego) have impermanent lakes associated with major floods overflowing into low-lying areas of floodplains (Jaensch, 1999).

Rivers and waterholes

As foreshadowed in the above description of Galilee subregion flow regime classification of Kennard et al. (2010), temporal patterns of water and of depth of water are the overriding drivers of ecological characteristics of aquatic community type, species diversity and species abundance (Silcock, 2009) – with spatial connectivity as a secondary (and often related) driver.

In the northern Flinders river basin, with its relatively reliable annual flow regimes, Leigh et al. (2010a) found the macroinvertebrate community to be ‘dynamically stable’, able to respond to relatively predictable change across seasons. By contrast, in rivers of the Lake Eyre Basin, those in the Bulloo and Paroo river basins, and the Warrego River (with their more irregular flow regimes), diversity of invertebrates, fish and birds at a broad scale follows a boom and bust cycle. Booms are associated with high-flow periods and better water quality (Shiel et al., 2006; Kingsford et al., 2010; Sheldon and Fellows, 2010) – or more specifically to sequences of flows that are able to fill all ‘hydrological sponges’ in a river system (Leigh et al., 2010b). For invertebrates and fish, booms result from population dynamics entirely within the river systems, but for nomadic waterbirds – which Kingsford et al. (2010) describe as ‘time and space travellers’ – diversity is not determined locally or by any one river system, but instead by the probability of viable resource patches across all river systems in inland Australia.

In the inland rivers, as floods recede and water flow is no longer continuous, waterholes and riverine wetlands take on the role of refugia, habitats to which a species population retreats and persists during times of environmental stress (Marshall et al., 2006; Silcock, 2009; Sheldon et al., 2010; Puckridge et al., 2010). Refugia during the dry period are important areas for the survival of species and persistence of water-dependent communities. Their physical habitat characteristics (e.g. surface area, depth, underwater benches, eroding banks and snags) influence aquatic species diversity and evenness. For example, fish community and macroinvertebrate composition changes with the size, depth and structural diversity of the refugia (Balcombe et al., 2006; Arthrington et al., 2010; Puckridge et al., 2010).

Connectivity within and between inland river systems is the spatial analogue of temporal variation in flow rate, and the two are interlinked as larger floods or flood sequences permit spatial connection between locations that are geographically and hydrologically more distant within a river basin. Balcombe et al. (2006), Leigh and Sheldon (2009), Fensham et al. (2011) and Kerezsy et al. (2013) have all emphasised the role of connectivity between, or conversely isolation of, waterholes and wetland refugia. Kerezsy et al. (2013) demonstrated that in the Georgina-Mulligan river basin, in the western Galilee subregion, connectivity interacts with life history strategies of fish, so that species can be identified as either extreme or conservative dispersers. Connectivity within river systems during times of flood has also been identified as the most probable reason for the low level of endemism observed in waterholes in inland river systems (Fensham et al., 2011).

However, isolation between river systems is also important for species distribution and endemism. For example, Australian smelt, carp gudgeon and Cooper Creek catfish occur only in the Cooper river system, while golden goby and banded grunter are only in the Georgina-Diamantina river system (Fensham et al., 2011; Kerezsy et al., 2013).

Despite the documented importance of connectivity along river systems, connectivity between aquatic and adjacent terrestrial ecosystems has been observed to be relatively weak. Using stable isotope techniques, Bunn et al. (2003) and Fellows et al. (2007), in the Cooper Creek, and Jardine et al. (2013) in the Flinders River, have found that aquatic food webs in waterholes during non-flow periods depend almost exclusively on autochthonous carbon sources from within the waterhole or falling into the waterhole from the littoral zone, and very little from surrounding terrestrial sources. Likewise Arthington et al. (2010) could find little influence of medium-scale ‘watershed’ characteristics on fish assemblage structure in waterholes.

Shiel et al. (2006) has shown the significance of water salinity in determination of zooplankton diversity and assemblage composition in the Lake Eyre Basin rivers. The study observed generally lower species richness in sites of higher salinity, but concluded that the effects of salinity were site-specific and involved thresholds of change. The authors suggested that the threshold level for salinity at a site was probably dependent on the time span between flushing events of fresher water relative to the life history characteristics and physiological tolerances of individual species.

On the east side of the Great Dividing Range, the Burdekin river basin stands somewhat in contrast to the other river basins described above. Pusey et al. (1998) found the fish fauna on the Burdekin River (above the dam) to have low diversity compared with other eastern river basins, but comprised of a combination of species with northerly and southerly distributions. With its more continuous flow, the key drivers of fish species composition were flow rate, substrate (sand versus gravel or cobble) and presence of snags and coarse debris, which lead to an upstream–downstream gradient of composition and abundance. An equivalent gradient may also occur along the Belyando River, a tributary of the Burdekin River in the east of the Galilee subregion.


Jaensch (1999) details a variety of types of swamps that are associated with the margins of rivers, oxbows, waterholes, lakes and springs, or the lower-lying parts of river floodplains. The dynamics and ecology of these wetlands is most likely determined primarily by surface water hydrology and seasonal or infrequent flooding from rivers and lakes, although in the wetland classes containing trees (e.g. Eucalypt wooded swamps and Acacia/belah wooded swamps), the trees are likely to be accessing groundwater. With the exclusion of the dependence of the trees on groundwater, the biodiversity and ecology of swamps are poorly studied in comparison with other wetland habitat types. Swamps are often mapped as terrestrial ecological communities and form part of the subregion’s complex clinal mosaic of vegetation shown in Figure 51.


Fensham et al. (2011) observed that rockholes are poorly known in the eastern Lake Eyre Basin. They document 18 permanent rockholes in three clusters in Tertiary sandstone ranges to the west and south of Winton (in the Diamantina and Cooper Creek catchments). Data were available on the biota of only five rockholes. All major groups of aquatic organisms had low diversity and abundance, and there was no evidence of endemism.

Outcrop springs

Fensham et al. (2011) mapped outcrop springs in three groups in the Cooper Creek catchment: between Windorah and Winton, between Windorah and Blackall, and north-east of Blackall, on the western slopes of the Great Dividing Range. More species were observed in outcrop springs than in rockholes, but all species observed were widespread. Geographically isolated populations of three species of plant, one species of mollusc (Sermyla sp.) and one species of fish (Mogurnda clivicola, the Flinders Ranges mogurnda) were observed, but no endemism was evident.

Discharge springs

Discharge springs have been studied to a much greater extent than outcrop springs. Fensham and Fairfax (2003) estimated that before 1900 there were 300 discharge spring complexes, or local clusters of springs, in the Great Artesian Basin (excluding Cape York Peninsula), of which only 36% (108 complexes) are still active. Most of these spring complexes lie within the Galilee subregion or, given the groundwater and surface water hydrology described in the previous sections, are likely to fall within the preliminary Assessment extent of potential development impacts from this subregion. Fensham et al. (2011) record 49 of those original spring complexes in the Georgina-Diamantina and Cooper Creek catchments of the Lake Eyre Basin, and 25 remain active. Because of their in-transit association with basement rocks, the water is generally alkaline (Fensham et al., 2011).

Because the groundwater has a very long residence time in the Great Artesian Basin, discharge springs show minimal fluctuations in flow rates, and their biota are adapted to relatively stable environmental conditions (i.e. there is low resilience and low resistance to environmental change in the biota).

Isolation of discharge springs complexes means that they have the highest rates of endemism of any surface aquatic habitat type (Fensham and Price, 2004; Fensham et al., 2011). Almost half of all species recorded from discharge springs in the Great Artesian Basin are endemic to the area. Jardinella, a genus of snail, is represented by 12 locally endemic species. Each of the three species of fish that are listed under the EPBC Act is restricted to a single springs complex. The significance of endemism led Fensham and Price (2004) to rank the discharge springs on degree of species endemism, as a basis for conservation prioritisation.

There is a substantial number of Great Artesian Basin discharge spring complexes in South Australia, to the west and south of Kati Thanda – Lake Eyre (see Greenslade et al., 1985; Zeidler and Ponder, 1989; Tyler et al., 1990; Harris, 1992). These springs are hydrologically connected to the Great Artesian Basin, but lie outside of the Galilee subregion. Their ecological characteristics are driven by similar factors and they also exhibit high levels of endemism.

Subsurface aquatic habitats

In the Galilee subregion, there is little information on the diversity and ecology of stygobiota, the suite of organisms that inhabit subterranean groundwater habitats. Humphreys (2006) and Tomlinson and Boulton (2010) report that the biodiversity of Australia’s subsurface groundwater-dependent ecosystems is inconsistently characterised. Invertebrates (especially crustaceans) are well characterised only in the major artesian basins of Western Australia, while microbial, fungal and protozoan diversity is virtually unexplored throughout Australia.

From the analysis of the ecological characteristics of groundwater environments by Tomlinson and Boulton (2010), it is, however, possible to identify, in principle, two sets of key drivers for subsurface ecosystems:

  • The stygobiota is adapted to relatively stable environmental conditions compared with surface aquatic environments (except Great Artesian Basin discharge springs), and thus is likely to depend strongly on the stability of the groundwater regime and other abiotic environmental factors (i.e. there is low resilience and resistance amongst stygobiota).
  • Because detritivorous microbes, rather than plants, are the basis of the food chain, ecosystem structure depends on carbon and nutrient inputs through vertical ecotones – the vadose zone in soil under terrestrial vegetation, and the hyporheic and littoral zones of springs, rivers and wetlands – and changes in resource fluxes through these ecotones could lead to change in stygobiota diversity and abundance. Recent change and threatening processes

Ecological changes to –and potentially threatening processes for – rivers, waterholes, rockholes and outcrop springs are poorly documented for the Galilee subregion. Choy et al. (2002) undertook a survey of the ecological condition of reaches of the Georgina and Diamantina rivers and Cooper Creek and concluded that they were in generally good condition except for bank damage by cattle. However, Silcock (2009) indicated that river waterholes are being slowly degraded by the cumulative impacts of cattle, feral animals, native herbivores and their consequent total grazing pressure during dry periods.

Non-native fish seem to be a lesser threat in the rivers of the subregion than in other parts of Australia. Costelloe et al. (2010) observed that non-native fish are disadvantaged by, and their invasions have been hampered by, the extremely variable flow regimes in Lake Eyre Basin rivers and wetlands.

Change in discharge springs have been the subject of much closer scrutiny, because of both the large number of springs that have become inactive and the sensitivity of the remaining active springs to ecological impact. The past and current threatening processes are (Fensham and Fairfax, 2003; Fensham et al., 2011; Kerezsy and Fensham, 2013):

  • drawdown of groundwater for stock, irrigated agriculture and mining – a significant driver of inactivity and diminishment of springs
  • excavation, including dredging, conversion to dams, wells, draining, and construction of raised concrete structures that limit surface flows away from the point of discharge. At least one form of excavation affects 26% of active springs (Fensham and Fairfax, 2003)
  • impoundments
  • exotic plants (23 species recorded by Fensham and Fairfax (2003)), including plant species for ponded pastures (e.g. Brachiara mutica, Echinochloa polystachya and Hymenachne acutiglumis)
  • pests, especially the mosquito fish (Gambusia holbrooki; see Kerezsy and Fensham (2013) for more details) and the cane toad (Bufo marinus)
  • feral animals, such as pigs, horses and donkeys (throughout the Great Artesian Basin area of Queensland), and camels (in western desert areas)
  • sheep grazing aquatic and littoral vegetation, and subsequent erosion of exposed soils (in southern areas).

Fensham and Fairfax (2003) record only three discharge spring complexes in national or conservation parks. Subject to effective management plans, park status affords those spring complexes protection against some of the threatening processes above, but aquifer drawdown is a more diffuse process that would also require coordinated management actions in surrounding lands regardless of designation. Species and ecological communities of national significance

Fifteen aquatic species are listed under the EPBC Act and are known to occur, or are likely to occur, in the Galilee subregion: six plants, three fish, one reptile, and five birds (Table 10). The three fish species and the plant Eriocaulon carsonii are exclusively associated with Great Artesian Basin discharge springs, while the other species are associated with a wider variety of aquatic habitats.

The community of native species dependent on discharge springs in the Great Artesian Basin is the principal aquatic ecological community listed under the EPBC Act for the subregion (Table 10). This community has become the focus of intense management concern as a result of its high levels of endemicity and the many potentially threatening processes that have been identified (e.g. Wilson, 1995; Fensham and Price, 2004; Queensland Environmental Protection Agency, 2005; Fensham et al., 2010; Fensham et al., 2011; Kerezsy and Fensham, 2013). Queensland Environmental Protection Agency (2005) provided a list of species of ‘conservation significance’ because they are dependent upon and confined to discharge springs (Table 13), but only some are also formally protected under either national or state legislation.

Table 13 Great Artesian Basin discharge springs species of conservation significance

Asset type

Scientific name

Common name

Ferns and allies

Thelypteris confluens

Cyathea exilis

Cyathea feline


Eryngium fontanuma

Thornless blue devil

Eriocaulon carsoniia

Salt pipewort or button grass

Myriophyllum artesiuma

Water or artesian milfoil

Hydrocotyle dipleuraa

Peplidium sp.


Sporobolus pamelaea

Spring grass or spring dropseed

Eragrostis fenshamii

Springs lovegrass

Arthraxon hispidus

Hairy-joint grass

Fimbristylis sp.

Fimbristylis blakei

Trees and shrubs

Calophyllum bicolour


18 species of freshwater snail (from the families Hydrobiidae, Bithyniidae and Planorbidae) including Jardinella isolata


Caridinia thermophila

Freshwater shrimp

Ponderella bundoona

Freshwater isopod

Ponderella ecomanufactia

Freshwater isopod


Chlamydogobius squamigenusa

Edgbaston goby

Chlamydogobius micropterusa

Elizabeth Springs goby

Scaturiginichthys vermeilipinnisa

Red-finned blue-eye


Epthianura crocea croceaa

Yellow chat (gulf subspecies)

Source data: Queensland Environmental Protection Agency (2005)aSpecies that also have national or state threatened status. Species of regional significance

For the 102 taxa (including some subspecies) listed under Queensland’s Nature Conservation Act 1992 but not also listed under the EPBC Act, there has been no formal assessment of which are associated with aquatic habitat types. However, it is possible to identify 12 taxa with clear water dependence using record and habitat data from the Atlas of living Australia (Atlas of Living Australia, 2014):

  • plants:
    • salt pipewort (Eriocaulon carsonii, all three subspecies)
    • Hydrocotyle dipleura (no common name)
    • artesian milfoil (Myriophyllum artesium)
    • spring grass or spring dropseed (Sporobolus pamelae)
    • Sporobolus partimpatens (no common name)
  • reptiles:
    • Emydura subglobosa ssp. worrelli (diamond-head turtle)
  • birds:
    • black-necked stork (Ephippiorhynchus asiaticus)
    • freckled duck (Stictonetta naevosa)
    • radjah shelduck (Tadorna radjah)
    • yellow chat (Epthianura crocea).

Last updated:
5 January 2018