3. Current status - DCQ · Draft Lake Eyre Basin State of the Basin Condition Assessment 2016 Report: for public consultation 18 3. Current status 3.1 Introduction This chapter presents

Draft Lake Eyre Basin State of the Basin Condition Assessment 2016 Report: for public consultation 18

3. Current status 3.1 Introduction

This chapter presents an overview of the current status of hydrology, water quality, fish

and waterbirds of the Lake Eyre Basin. Because of the highly variable nature of the Basin,

as well as the general lack of long-term information, this chapter does not attempt to

evaluate ecological condition based on historical records or ‘reference’ sites. Rather, the

information presented here provides a baseline from which future changes can be

assessed within the context of natural variability or in relation to pressures and threats

such as climate change. Additionally, findings are interpreted in relation to current

ecological understanding and knowledge of environmental responses to human pressures

to ascertain a general picture of the Basin’s current condition. Where relevant, this

assessment is also informed by comparisons with neighbouring regions such as the

Murray-Darling Basin. It should be noted that the previous assessment of the Basin’s

condition produced in 2008 did not provide a quantitative baseline against which

changes in condition might be assessed.

3.1.1 Knowledge sources and approach

The information presented in this chapter was compiled from a wide range of sources

(Table 1). The sources especially included data collected under the Lake Eyre Basin Rivers

Assessment program, which fish communities, water levels and water quality at 53

waterholes across the Basin between 2011 and 2016 (Figure 1; Appendix 1). Surface

water hydrology was also examined using available flow records from a range of

representative gauging stations located in the upper and lower reaches of the Cooper,

Diamantina and Georgina Rivers and from available gauging stations of the Finke,

Macumba and Neales Rivers. Water quality was reviewed from State-based databases,

quantitative analyses being limited to data on nutrient measurements. Waterbird status

was informed by data collected under the Eastern Australian Waterbird Survey, which has

monitored waterbird communities at 10 major wetlands in the Basin since 1983

(Kingsford et al. 2013). Knowledge from other published studies was also considered

where relevant (Table 1).

Status assessments are made on the basis of expert evaluation of available data with

respect to current scientific understanding. Each section in this chapter (hydrology, water

quality, fish and waterbirds) takes a different approach to evaluating status, largely due to

differences in data availability and quality. In most cases, the overall approach involves

the assessment of patterns of key attributes in space and time and evaluation of these

patterns in relation to climate, hydrology or human pressures. Particular attention has

been given to ascertaining the likelihood of any longer-term trends, especially declines, in

the status of these ecological components. Where relevant, status is also considered in

relation to the limits of acceptable change set for the Coongie Lakes Ramsar site to alert

managers to potential changes in ecological character under the Ramsar Convention on

Wetlands (DEWHA 2008; Butcher & Hale 2011).


3.1.2 Aboriginal engagement

The third Lake Eyre Basin Aboriginal Forum held in Birdsville, Queensland, in 2009

highlighted ‘the need for water planning processes in all Basin jurisdictions to engage

Aboriginal people, including through Aboriginal and other community education and

participation in the Lake Eyre Basin Rivers Assessment’. In response, jurisdictions began a

process of engagement supported by a review commissioned by Department of

Environment, Water and Natural Resources to explore how the Lake Eyre Basin Rivers

Assessment programme could bring together scientific and culturally appropriate

approaches to assessing the condition of rivers (Nursey-Bray 2015). This review

highlighted the following points and conclusions.

Water is of paramount importance to Aboriginal people in the Basin, representing a

composite of values that is socially and culturally significant. Aboriginal views are

underpinned by the notion of ‘Country’, which reflects a seamless connection between

people, land and waters. Water is not split up into different aquatic ecosystems, or indeed

legal jurisdictions, as is the case in Western classification, but understood as one resource

with multiple sites within the Country. The idea of health here is important. Unlike Western

classification systems, cultural and ecological indicators are not separated but woven

together. For example the finch (katyapara) is of particular significance to the Arabana and

features as a symbol in representations of their culture. For Arabana people, the presence

of finches represented not just ecological but also cultural health of a water site (Nursey-

Bray 2015).

The review further explored how the Lake Eyre Basin Rivers Assessment programme could

bring together scientific and cultural approaches and whether their integration through a

'one-model-fits-all' template was appropriate. Integration implies the incorporation of

Indigenous knowledge into current jurisdictional and institutional arrangements, but they

may simply not fit. The alternative notion of co-existence recognises that both parties are

equal and that each knowledge system is legitimate. The outcomes of Nursey-Bray’s (2015)

study suggested an appropriate model within which both cultural and scientific knowledge

about the region can co-exist, without being subsumed one into the other. It proposed an

approach by which cultural and scientific assessment approaches occur side-by-side,

bringing the strengths of each to the process.

The jurisdictional officers from Northern Territory, Queensland and South Australia

involved in the Lake Eyre Basin Rivers Assessment programme worked together with the

Aboriginal communities in the following ways.

In the Northern Territory, Central Land Council staff supported involvement of Tjuwanpa

Rangers from the Western Arrernte people. In Queensland, Lake Eyre Basin Rangers of the

Dugalunji Aboriginal Corporation participated in the monitoring programme. In South

Australia the Arabana helped develop an appropriate engagement model, and the

Adnyamathanha and the Aboriginal community of Oodnadatta participated in field

education events about the Lake Eyre Basin Rivers Assessment programme. At the Lake

Eyre Basin Aboriginal Forum in Tibooburra New South Wales, 2011, a description of the

Lake Eyre Basin Rivers Assessment programme was presented in a question-and-answer

session. Through these events productive discussions and an understanding of each other’s

cultural domains were progressed and continue to be developed.

The conclusions of Nursey-Bray (2015) highlighted two dimensions required for further


progress in Aboriginal engagement in monitoring and evaluation, as follows.

1. Support for Indigenous rangers to institute ongoing cultural monitoring on their

country across their water sites and;

2. Ensuring that such monitoring builds community capacity.

Image 5 Water quality sampling for the Lake Eyre Basin Rivers Assessment programme. Photo: D McNeil


Table 1. Summary of sources used to inform assessments of hydrology, water quality, fish and waterbirds for the Lake Eyre Basin State of the Basin

Report 2016. Theme Data sources Spatial extent Temporal extent Key references Hydrology Australian Water Availability

project Basin wide 2008-2015 http://www.csiro.au/awap

State gauging stations Representative / available stations from Cooper, Diamantina, Georgina, Finke, Macumba & Neales

2007-2015 https://water-monitoring.information.qld.gov.au/; https://nt.gov.au/environment/water/water-data-portal; https://www.waterconnect.sa.gov.au

Longer-term trends

State gauging station Cullyamurra, Cooper Creek

1973-2015 https://www.waterconnect.sa.gov.au

Groundwater interactions

High Ecological Value Aquatic Ecosystems sub-project

Mid-Finke waterholes Duguid 2013

Published study Neales 2011-2015 Costelloe et al. 2005 Waterhole hydrology

Lake Eyre Basin Rivers Assessment program

53 waterholes across Basin (see Figure 1)

2011-2015 Cockayne et al. 2012; Cockayne et al. 2013; Duguid et al. 2016; Mathwin 2015; Sternberg et al. 2014

Queensland waterhole modelling

Published studies Water quality2*

State datasets (from gauging stations); only datasets including nutrient data used

Multiple sites in Cooper, Diamantina-Georgina catchments

1970s - 2015 https://wetlandinfo.ehp.qld.gov.au/wetlands/assessment/monitoring/current-and-future-monitoring/

Monitoring River Health Initiative; Australian Rivers Assessment Program

Multiple sites in Cooper, Diamantina-Georgina catchments

1994-1999 http://pandora.nla.gov.au/tep/25389

Published studies Cooper 2001-2004 Sheldon & Fellows 2010 Diamantina-Georgina Williams et al. 2015 Diatom study 17 sites in Cooper and

Diamantina (Queensland)

20154 Sternberg et al. 2015

http://www.csiro.au/awap

https://water-monitoring.information.qld.gov.au/

https://nt.gov.au/environment/water/water-data-portal

https://nt.gov.au/environment/water/water-data-portal

https://www.waterconnect.sa.gov.au/

https://www.waterconnect.sa.gov.au/


Theme Data sources Spatial extent Temporal extent Key references Fish Lake Eyre Basin Rivers

Assessment monitoring data Cooper, Diamantina-Georgina, Finke, Macumba and Neales catchments

2011-2016 Cockayne et al. 2012; Cockayne et al. 2013; Duguid et al. 2016; Mathwin et al 2015; Sternberg et al. 2014

Waterbirds Eastern Aerial Waterbird Survey

Cooper wetlands – Lower Cooper, Lake Dunn, Lake Galilee, Lake Hope, Lake Yamma Yamma, Diamantina-Georgina – Goyders Lagoon, Lake Katherine, Lake Mumberry, Lake Phillippi, Lake Torquinnie

1983-2016 Kingsford et al. 2013

Coongie Lakes survey Innamincka Regional reserve

2008 Kingsford et al. 2012

* N.B. Water quality data were also collected under the Lake Eyre Basin Rivers Assessment programme but were not compiled for the quantitative analyses discussed here;

however, they were used to inform the assessment. Water quality data from the Lake Eyre Basin Rivers Assessment are available from this programme’s annual reports

(Cockayne et al. 2012; Cockayne et al. 2013; Sternberg et al. 2014; Mathwin et al 2015; Duguid et al. 2016).

1. Assessment of hydrological status was conducted by Justin Costelloe, University of Melbourne.

2. Assessment of water quality status was conducted by South Australia Environment Protection Authority, Northern Territory Department of Environment and Natural

Resources, John Tibby (University of Adelaide) and Queensland Department of Natural Resources and Mines.

3. Assessment of fish community status was conducted by South Australian Research and Development Institute, Northern Territory Department of Environment and Natural

Resources and Queensland Department of Natural Resources and Mines in consultation with Angela Arthington (Griffith University).

4. Assessment of waterbird status was conducted by Richard Kingsford and Gilad Bino (University of New South Wales).


3.2 Hydrology

3.2.1 Key messages

Rivers in the Lake Eyre Basin are among the most hydrologically variable in the world

and are, on average, about twice as variable as those from other arid zones. In

considering the hydrology of the Basin the following observations have been identified:

• Hydrology of the Basin between 2008 and 2016 was shaped by two contrasting

periods; a mostly wet period between 2009 and 2012 and a predominantly dry

period from 2012 to 2015. Wetter conditions returned to much of the Basin in

2016, and earlier (January 2015) in the Georgina, Macumba, Finke and Warburton.

• Streamflow records are too short and too variable to detect any long-term changes

in surface water hydrology; although given the current relatively low level of water

resource development it is considered that, for much of the Basin, the surface

water flow regime is near natural condition.

• Interactions between surface and ground waters remain poorly understood.

Evidence suggests that groundwater is likely to make important contributions to

the hydrology of some Basin waterholes. Streamflow is also likely to be an

important source of recharge for both deep (Great Artesian Basin) and shallow

ground waters which are ecologically significant because they sustain spring

ecosystems and riparian trees respectively.

• Considerable advances have been made as a result of monitoring by the Lake Eyre

Basin Rivers Assessment programme, in addition to previous natural resource

management studies such as ARIDFLO, in understanding waterhole hydrology.

Relationships between maximum depth at cease-to-flow and persistence, and

between surface area and volume, have been identified; they enable patterns of

aquatic habitat availability to be more accurately mapped in space and time.

• None of the limits of acceptable change for hydrology of the Coongie Lakes

Ramsar site were breached between 2011 and 2016, although one was

approached during the recent period of low flows in the lower Cooper.

3.2.2 Recent surface water patterns

Surface water hydrology in much of the Lake Eyre Basin between 2008 and 2016 was

dominated by two contrasting climatic periods:

• predominantly wet conditions associated with a large La Niña episode between

2009 and 2012

• predominantly dry conditions from 2012 to 2015 resulting in drought across much

of the Basin (Figures 4 & 5).

The wet period between 2009 and 2012 encompassed several large flood events

including, in 2010, the third largest flood on record at Cullyamurra on Cooper Creek

(Figure 5). Large floods were also experienced in many Basin catchments in 2011. In

some of the western catchments and in the upper reaches of some eastern catchments,

the 2011 floods were larger than those experienced in 2010. The 2010-2012 wet period

(which started as early as 2009 in some of the north-western catchments, e.g.


Georgina) resulted in long periods of hydrologic connection between the upper and

lower reaches of catchments as well as extensive floodplain inundation. At Cullyamurra

on the lower Cooper Creek, for example, continuous flow occurred between 2010 and

2011 for the first time on record. Significant connectivity also occurred between

catchments during this wet period with the Georgina River flowing into the Diamantina

and the Neales and Warburton-Diamantina flowing into Lake Eyre in 2011.

In contrast, much of the Basin experienced drought conditions throughout the 2013-2015

period with only small annual floods occurring in the lower reaches of the major rivers

(Figures 5 & 6). Amongst the longest periods of no flow on record were observed during

this time in the upper Cooper (Thomson and Barcoo Rivers) and the western catchments

(Finke, Macumba and Neales Rivers). In the Neales River, two years without any

streamflow were recorded while three years without flow were observed in the lower

Finke. Most aquatic habitats in the western catchments dried out as a result. Other than

those fed by Great Artesian Basin springs, Algebuckina Waterhole was the only waterhole

to retain water in the Neales catchment during this period, but even this reached critically

low levels. In the upper and mid reaches of the Finke River, periods of low flow of two or

less years were recorded depending on location, although many waterholes still persisted.

Partial alleviation of the 2013-2015 drought occurred in 2014 and 2015 with some

rainfall and streamflow in the northern and north-western catchments (Georgina) and

flooding in the Macumba in 2015. A return to wetter conditions has continued into 2016

with floods occurring in most Basin catchments.

Image 6 Data logger used in waterhole sampling for the Lake Eyre Basin Rivers Assessment programme. Photo: B Cockayne


Figure 5 Total rainfall across the Lake Eyre Basin in each 'water year' (1 October to 30 September) from 2008 to 2015. Mean annual rainfall across the Basin (average) is also shown, illustrating that 2010 and 2011 were wetter than average while 2008 and 2013-14 were drier than average. Source: Australian Water Availability project, Bureau of Meteorology (www.csiro.au/awap).


Figure 6 Hydropgraphs at representative guaging stations of upper and lower reaches of major Lake Eyre Basin streams (Cooper, Diamantina and Georgina Rivers) and from available stations on the Finke, Macumba and Neales Rivers. Note the data on water level only, rather than discharge, are available for the Macumba and Neales. Where gauging sations have sufficiently long records, the annual recurrence interval of each flood year is also shown on the hydrograph by numbers above bars. Grey dots represent Lake Eyre Basin Rivers Assessment sampling dates.


3.2.3 Longer-term surface water trends

Discharge data from gauging stations in the Lake Eyre Basin are too short, intermittent and

variable to allow the identification of any long-term changes in surface water flows. The

gauging station at Cullyamurra on Cooper Creek, for example, has been operating since 1973

and this 43 year record demonstrates the very high variability typical of Basin rivers

(Figure 7). The hydrograph at this gauging station is dominated by large flood events and

does not exhibit any significant trend in annual streamflow over time. Nor can hydrologic

models be used to identify long-term changes in runoff and streamflow in the Basin for

similar reasons, i.e. insufficient duration of records for model calibration and high levels of

uncertainty in model outputs.

Figure 7 Hydrograph of Cooper Creek at Cullyamurra guaging station showing daily discharge in megalitres per day between 1973 and 2015.


Image 7 Cullyamurra waterhole in June 2013. Photo: S Colville

3.2.4 Groundwater interactions

Interactions between surface and ground waters in the Lake Eyre Basin are poorly

understood. There is little evidence that groundwater discharge sustains river flows in

the Basin except in a few reaches during particularly wet periods. In the Finke River

periods of persistent flow have been documented along long sections, especially in the

wet periods of 2000-2001 and 2010-2011, which may have been sustained by elevated

watertables (Duguid 2013). Groundwater discharge is most likely to contribute to

streamflow in the upper reaches of catchments, although saline groundwater discharge

has been observed following large flood events in the mid reaches of the Neales

catchment (Costelloe et al. 2005) and in the Warburton sub-catchment of the Diamantina.

Groundwater discharge also contributes to sustaining water levels in some waterholes in

the Basin. In the lower reaches and western catchments, groundwater discharge is

typically saline. Consequently, waterholes affected by groundwater discharge often reach

hypersaline levels within 6 to 12 months after flow ceases (Costelloe & Russell 2014). In

Queensland, modelling has been conducted on 17 waterholes using observed water level

data and modelled evaporation rates. Results suggest that none of these waterholes has

any significant groundwater inputs but they do contribute to recharging of the

unconfined groundwater table. Some deep waterholes, such as Cullyamurra and Nappa

Merrie on the Cooper, have depths reaching 11 to 25 m and are therefore highly likely to

intersect the water table. Similarly, some waterholes in the mid-Finke are as deep as 11

m (Duguid 2013). The extent of groundwater exchange in these important freshwater

habitats, has not been quantified.

Streamflow in the Basin contributes to the Great Artesian Basin. Recharge to the Great

Artesian Basin from the lower reaches of the Finke River is likely to be particularly


important as it contributes substantial volumes to the flow path that discharges into the

Dalhousie Springs complex (Fulton 2012). Even small rates of recharge to local alluvial

aquifers are critical to maintaining sufficient fresh groundwater to sustain riparian trees,

as observed in the Cooper, Diamantina and Neales catchments (Cendón et al. 2010;

Costelloe et al. 2008).

3.2.5 Waterhole hydrology

Significant advances have been made since 2008 in understanding the physical and

hydrologic character of waterholes in the Lake Eyre Basin, especially in the Neales,

Cooper and Diamantina in South Australia, the Thomson River in Queensland and the

Finke River in the Northern Territory (Figure 8). Detailed information is now available on

the location and bathymetry of waterholes in these reaches as well as their hydrologic

persistence, such as maximum depth at cease-to-flow, frequency of inflows and

groundwater connectivity. This knowledge is important for understanding the

distribution, quality and persistence of aquatic habitat and significant refuges for aquatic

fauna such as fish.

Studies of waterhole bathymetry and hydrology in some Queensland and South

Australian waterholes indicate that maximum depth at cease-to-flow provides a

reasonable indicator of how long waterholes are likely to persist in the absence of

surface inflows (Costelloe & Russell 2014; Costelloe et al. 2007). A strong relationship

between surface area and volume, but not surface area and persistence, has also been

identified amongst some Queensland waterholes, allowing waterhole volumes to be

estimated from satellite imagery.

Deep waterholes (i.e. greater than 6.6 m deep and capable of persisting over three years

without surface inflow) are absent from most of the western Basin catchments other

than the Finke (Figure 8). In the Neales catchment, for example, Algebuckina waterhole is

the deepest and most persistent waterhole and is a critical refuge for larger bodied fish

that cannot persist in shallow Great Artesian Basin springs. By the end of 2014, it was the

only waterhole retaining water in this catchment and nearly dried out following two

years without streamflow.

Cullyamurra Waterhole on the lower Cooper is the largest and deepest waterhole in the

Basin with a maximum depth of around 23.2 m. The reach of the Cooper containing

Cullyamurra (from around Nappa Merrie Waterhole to the junction of the Main Branch

and Northwest Branch) also has the highest density in the Basin of deeper waterholes

(greater than 4.4 m at cease-to-flow). As a result of these deep waterholes and

consistently good water quality, this reach is likely to provide long-term refuges for fish.


Figure 8 Distribution of waterholes in the Lake Eyre Basin with measured cease-to-flow depths (CTFD) in metres. Waterholes with cease-to-flow depths of 2.2 - 4.4 m can persist for more than one year without flow; those with cease-to-flow depths of 4.4 - 6.6 m for two years without flow; and those with cease-to-flow depths greater than 6.6 m for more than three years without flow.

3.2.6 Coongie Lakes

Under the Ramsar Convention of Internationally Significant Wetlands, limits of acceptable

change have been defined for hydrological changes in the northwest branch of Cooper

Creek that feeds the Coongie Lakes in South Australia (Table 3; Butcher & Hale 2011).

These have not been triggered. However, the low flows in the lower Cooper over the past

four years have approached one limit of acceptable change relating to Lake Goyder (Table

2). It is difficult to assess the two limits of acceptable change relating to waterhole

persistence (numbers 4 and 5 in Table 2) because conditions in these waterholes are not

effectively monitored by the Landsat record and do not have specific monitoring sites to

measure water level variations.


Table 2. Assessment of hydrological limits of acceptable change for the Coongie Lakes Ramsar area (Butcher & Hale 2011).

Limits of acceptable change

Status

Evidence

1. Coongie Lake receives inflows no less

than eight times in any ten year period,

with no dry period lasting longer than

12 consecutive months

Within

Coongie Lake has received inflow in every year of the Cullyamurra record (1973-2016). The smallest annual flow

through Cullyamurra was in 1985 (gigalitres total). Modelling and Landsat data indicate that a small amount of

inflow occurred to Coongie at this time (Costelloe et al. 2004). Logger data at Kudriemitchie show that Coongie has

received inflow during the low flow years of 2013-2015.

2. Lake Goyder receives inflows no less

than six times in any ten year period,

with no dry period lasting longer than

30 consecutive months

Nearly

exceeded

Lake Goyder did not receive inflow in the 2013-2016 period according to the Landsat record, although some

minor flows may have occurred that could not be detected. This is the longest dry period in the Cullyamurra

record for this lake and it has been dry since December 2013 (30 months). However, the Lake has received

inflow in six of the last ten years.

3. Large flood events occur no less than

four times in any 30 year period (as

defined by Costelloe 2008)

Within

The Cullyamurra record shows that large flood events (more than 38 gigalitres/day) known to cause

outflow from the Coongie Lakes system have occurred 10-11 times in the past 43 years and 6-7 times in the

past 30 years.

4. No drying of any permanent

waterholes

Within

Permanent waterholes are classified as those that typically receive inflow annually and have cease-to-flow

maximum depths of greater than 4 m. These are restricted to Cooper Creek (Cullyamurra to Marpoo) and the

Northwest Branch distributary (Scrubby Camp, Kudriemitchie). Embarka Waterhole on the Main Branch is also

in this category as it is the only deep waterhole (cease-to-flow depth of 3.8 m) that receives annual inflow on the

Main Branch.

Given that Coongie Lake received flow in every year of the Cullyamurra record, there has been no drying of

permanent waterholes on Cooper Creek or the Northwest Branch. Embarka Waterhole requires approximately

1500 megalitres/day at Cullyamurra for inflow and there have been at least two years in the record where this

was not received (1982, 1985) but the no flow period of 14-18 months would not have resulted in the drying of

this waterhole.

5. No drying of semi-permanent

waterholes to less than 70%of time

inundated over any 20 year time period

Not known

This limit of acceptable change is difficult to assess without particular semi-permanent waterholes being identified with a known maximum cease-to-flow depth and long term frequency of inundation. Semi-permanent waterholes on the Northwest Branch (i.e. in the connecting channels of the lakes) could be nominated, as could some of the deeper waterholes on the Main Branch downstream of Embarka Swamp (e.g. Narie, Cuttapirie Corner, Parachirrinna). Large downstream lakes, such as Lakes Hope, Killamperpunna and Killalpaninna, would be unlikely to meet this limit of acceptable change.


3.3 Water quality

3.3.1 Key messages

• No major deterioration of water quality has been observed in the Lake Eyre

Basin since the 2008 assessment. Water quality is strongly influenced by river

flow, evaporation and groundwater connection. Water quality in the Basin is

dependent on the natural flow of the rivers and their management.

• The conductivity (i.e. salinity), turbidity and nutrient levels of the Lake Eyre Basin

rivers are highly variable, both temporally and spatially. Most waters are alkaline,

and dominated by bicarbonate and sodium ions.

• Existing national water quality guidelines are unsuitable for evaluating water

quality in the Lake Eyre Basin due to the variable river conditions. Levels of

nutrients and turbidity are higher than the guidelines and higher than many

Australian rivers. New guidance is currently under development for Australia’s

temporary waters.

• Streams of the northern and eastern Lake Eyre Basin (the Cooper and Georgina-

Diamantina) tend to be mostly fresh, nutrient-enriched, turbid and slightly alkaline.

Waterholes in the lower reaches of these catchments tend to be less turbid and

become more saline between flows.

• In some parts of the Basin, nutrient concentrations and turbidity could be higher

than natural levels. Further work is necessary to gain a better understanding of

turbidity and nutrient dynamics. High salinity in some parts of the Basin is a natural

result of the arid climate.

3.3.2 Overview

The Lake Eyre Basin Rivers Assessment programme monitored the water quality of 50

sites from 2008 in spring and autumn every year. Water quality is strongly influenced by

patterns of flooding and drying and is therefore highly variable in both time and space

(Sheldon & Fellows 2012). Because of the variable conditions, water quality sampling in

the Basin most often occurs when rivers and streams are not flowing, and reduced often

to long, disconnected pools. The high levels of variability also present a challenge for

establishing threshold levels for acceptable water quality.

Default stressor trigger values listed in the national water quality guidelines (ANZECC &

ARMCANZ 2000) tend to be unsuitable for the arid, temporary rivers of the Lake Eyre

Basin (Choy et al. 2002; Sheldon & Fellows 2010). Many Basin watercourses, for

example, exhibit higher turbidity and nutrient concentrations than most other streams in

Australia and New Zealand (ANZECC & ARMCANZ 2000) and also exceed those of arid

streams in the United States (Evans-White et al. 2013). Similarly, limited trace element

data available for the Basin indicate that the soluble copper, soluble zinc and aluminium

concentrations in many sites have often been above the toxicant values for 90% species

protection listed in the national water quality guidelines (ANZECC & ARMCANZ 2000).

However, these measurements probably reflect the natural composition of clays in the

catchment rather than any widespread human source of contamination (Williams et al.

2015). New guidelines are currently being developed for Australia’s temporary waters

and work is underway to develop a framework for locally derived guidelines.

Available water quality data indicate some general patterns between catchments, as well


as between and within some sub-catchments. Rivers and creeks in the eastern and

northern rivers are mostly fresh (i.e. less than 500 micro-Siemens/cm conductivity),

turbid (100-500 nephelometric turbidity units) with high suspended solids (greater than

100mg/L), slightly alkaline (pH greater than 7) and tend to be dominated by bicarbonate

and sodium ions and enriched with nitrogen (greater than1 mg/L) and phosphorus

(greater than 0.1 mg/L; Table 3). Within the Diamantina catchment, nutrient

concentrations increase downstream along the main channel with elevated phosphorus

concentrations detected in the Warburton River in the lower Diamantina (Table 5).

Colour, an indirect measure of dissolved humic acids and tannins, is variable among

rivers but low overall.

In the Cooper catchment, Torrens Creek exhibits notably high concentrations of nitrogen

and also greater turbidity than the remaining catchment (Table 3). The source of

nutrients over such a large spatial area is unknown but typical values recorded for most

streams in the Basin are higher than those listed for desert streams elsewhere (Smith et

al. 2003; Evans-White et al. 2013), contrasting with predictions of low nutrient levels for

desert streams (Dodds et al. 2015). All but one site monitored exceeded the turbidity

trigger of 100 nephelometric turbidity units with 42% of the sites exceeding the nitrogen

trigger value of 1 mg/L and 79% of sites exceeding the phosphorus trigger value of 0.1

mg/L.

Conductivity and salinity tend to be higher in the western rivers of South Australia and

the Warburton River than in the eastern and northern rivers (Table 3), and are

attributable to groundwater sources of salt. In the Finke River, salinity is particularly

variable. Freshwater pools are present in the upper parts of the catchment, whereas in the

middle reaches pools exhibit a wide range of salinities up to hypersaline, suggesting more

complex interactions between surface and ground waters than in other Basin rivers.

3.3.3 Temporal trends

Temporal patterns in available water quality data are highly variable across the Basin. No

clear temporal trends in water quality are apparent even in the relatively long-term

datasets from the Cooper and Diamantina-Georgina catchments, some of which extend

back to the 1970s. In Cullyamurra Waterhole in the Cooper Creek, for example, changes in

salinity and nutrients have fluctuated considerably since 1973, probably in relation to

hydrologic conditions (Figure 9).

Pronounced short-term patterns in salinity have been observed in some waterholes,

especially in the Finke, Neales and Diamantina Rivers, and are attributable to a

combination of evaporation and groundwater discharge (A. Duguid, personal

communication). Changes at individual sites are also strongly influenced by flow patterns.

At some sites, especially in the Finke River (Duguid 2013), large flows appear to increase

the influence of relatively fresh alluvial aquifers, offsetting temporally the effects of more

saline groundwater sources on waterholes following flows. The opposite pattern is

observed in the Neales and Diamantina, where large floods raise the unconfined saline

groundwater table and result in high salinity discharge into the channel during low flows

of the flood recession (Costelloe et al. 2005). In the typically low salinity waters of the

mid and upper Cooper, Diamantina and Georgina catchments, patterns of increased

salinity (although still low overall) have also been recorded between flows (Duguid et al.

2016; Mathwin et al. 2015; Sternberg et al. 2014).


Table 3. Water quality for some catchments of the Lake Eyre Basin. Mean values ± standard deviations except pH which is the median and the 10th and 90th

percentiles in parentheses. NA, data not available. The Finke River waterholes are located in the upper half of the catchment.

Catchment Subcatchment Electrical conductivity (µS/cm @25

°C)

Salinity (mg/L)

pH Turbidity (nephelometric turbidity unit)

Total suspended

solids (mg/L)

Colour (Hazen

unit)

Total nitrogen (mg/L)

Total phosphorus

(mg/L)

Cooper Creek Catchment

(eastern catchment)

Torrens Creek 219 ± 128 138 ±53 7.1 (6.8-7.4) 959 ±748 163 ±96 77 ±46 2.8 ±1.37 0.58 ±0.30 Thomson River 175 ± 156 112 ±

82 7.3 (6.8-7.9) 528 ± 588 268 ± 343 45 ± 58 0.87 ± 0.57 0.25 ± 0.15

Barcoo River 327 ± 283 206 ± 171

7.5 (7.0-8.5) 275 ± 460 255 ± 478 36 ± 31 0.85 ± 0.38 0.26 ± 0.25

Cooper Creek (QLD)

214 ± 122 133 ± 69

7.5 (7.1-7.8) 549 ± 468 221 ± 269 17 ± 15 1.87 ± 1.59 0.47 ± 0.39

Cooper Creek (SA) 228 ± 176 124 ± 100

7.6 (7.2-8.1) 391 ± 243 67 ± 43 48 ± 37 1.31 ± 0.76 0.47 ± 0.40

Georgina- Diamantina Catchments (northern

catchment)

Burke River 212 ± 109 123 ± 65

7.6 (7.4-7.9) 95 ± 60 102 ± 267 27 ± 27 0.55 ± 0.21 0.07 ± 0.04

Georgina River 478 ± 497 301 ± 302

7.6 (7.0-7.8) 194 ± 201 81 ± 108 12 ± 11 0.85 ± 0.34 0.17 ± 0.11

Diamantina River – Upper

190 ± 59 123 ± 35

7.7 (7.2-8.1) 423 ± 174 180 ± 133 10 ± 4 0.92 ± 0.55 0.29 ± 0.09

Diamantina River – Mid

127 ± 71 84 ± 37 7.4 (6.9-7.8) 689 ± 663 435 ± 440 36 ± 31 1.16 ± 0.79 0.44 ± 0.23

Diamantina River – SA

262 ± 34 NA 7.6 (7.4-8.0) NA NA NA 1.84 ± 0.43 2.05 ± 0.35

Warburton Creek 1024 ± 1068 NA 8.1 (7.8-8.3) NA NA NA 1.12 ± 1.09 4.38 ± 1.31

Western catchments

(South Australia)

Macumba, Neales, Peake & Lindsay Rivers

6250 ± 17532 NA NA NA NA NA 1.68 ± 0.67 0.1 ± 0.06

Finke River Low salinity waterholes

1,610 ± 1,350 NA 7.9 76 ± 59 NA NA NA NA

High salinity waterholes

11,360 ± 12,030 NA 8.0 24 ±23 NA NA NA NA


Figure 9 Salinity (top) and major nutrients (bottom) recorded in Cullyamurra Waterhole in the lower Cooper catchment between 1973 and 2007.


3.3.4 Biological indicators

Diatoms are a class of aquatic algae that tend to respond strongly to water quality. They are an

important part of many aquatic food webs and have been used extensively as an indicator of

water quality in Australia and around the world. The composition of diatoms in rivers is

usually influenced by salinity, pH and nutrient status (Sonneman et al. 2000).

A total of 196 diatom taxa were identified from 17 Queensland waterholes in the Lake Eyre

Basin in a study linking diatoms to water quality (Sternberg et al. 2015). Diatom communities

were characterised by taxa with a high nutrient tolerance. Of the five most abundant taxa, three

(Luticola goeppertiana, Gomphonema parvulum and Nitzschia palea) have nutrient preferences

that include the most nutrient-enriched category of streams in south-eastern Australia

(Sonneman et al. 2000). Other abundant taxa (Navicula schroeterii and Gomphonema parvulum)

have lower, but wide ranging, nutrient preferences.

A relationship between the composition of diatom communities and nutrients was identified,

with some taxa more abundant at sites with lower nutrient levels and other taxa more

abundant in higher nutrient sites. Total phosphorus explained the largest amount of variation

in diatom communities with magnesium the only other influential water quality variable.

Relationships between diatoms and pH and salinity are generally stronger than those found

with respect to total phosphorus (Tibby 2004). In the Basin, the reverse was found,

highlighting the response of diatoms and their potential use as indicators of water quality.

3.3.5 Condition

In the State of the Basin 2008: Rivers Assessment , Lake Eyre Basin catchments were assigned

either a ‘good’ water quality condition or were not rated due to insufficient information. Expert

review was required because suitable guidelines for arid rivers had not been developed at the

time. Locally derived reference sites were selected based on biological data, and included sites

subject to dryland grazing but excluded sites influenced by other pressures and threats

(intensive agriculture, industry, urban areas, point source discharges, or changes in flow).

Consequently, catchments were assigned ‘good’ water quality ratings despite recognition that

nutrient levels were high at many sites (Lake Eyre Basin Scientific Advisory Panel 2009).

No major deterioration of water quality has been observed in the Basin since the 2008

assessment. However, this assessment is hampered by the naturally high variability of water

quality and patchiness of the water quality data. Nutrient concentrations and turbidity could

have exceeded naturally high levels and been caused by human activity, though a better

understanding of these factors is required to be certain. The high salinity evident in some parts

of the Basin is likely to be a natural feature of the arid landscapes drained by these rivers,

driven by high evapotranspiration rates relative to low rainfall and infrequent streamflow, as

well as the groundwater supply of salts to river pools.


3.4 Fish

3.4.1 Key messages

• A large and extensive fish database has been provided by the Lake Eyre Basin

Rivers Assessment programme. Building on past work, including the ARIDFLO

project (Costelloe et al. 2004) and the Dryland Rivers project (Bunn et al.

2006), the database greatly improves understanding of the distributions and

population dynamics of fish species and the condition of fish communities.

• Fish communities are generally in good condition across the Basin, with

riverine environments supporting 19 native fish species including the Lake

Eyre yellowbelly and Barcoo grunter and three catfish species, including the

endemic Cooper Creek tandan. Other endemic riverine fish species include

Welch’s grunter, desert goby and Finke goby.

• A rapid range expansion has occurred in the Cooper Creek catchment of sleepy

cod, a translocated native fish that is foreign to the Basin. The population was

initially observed in the Thomson River and has expanded over six years

downstream to Coongie Lakes in South Australia. Previous translocations of

sleepy cod in Australia have resulted in rapid colonisation of the receiving

environment, followed by a decline in species with similar niche requirements,

yet it is currently unknown how this species will affect the native fish of the

Basin.

• Although fish communities in the Basin are generally in good condition,

work conducted under the Lake Eyre Basin Rivers Assessment programme

has identified exotic and translocated species as a threat.

3.4.2 Fish distributions

Twenty-nine fish species have been recorded historically in riverine habitats of the Lake

Eyre Basin (Table 4). A further ten species are found exclusively within springs were not

monitored as part of Lake Eyre Basin Rivers Assessment programme. Of the riverine

species, 22 species, including 19 natives and three translocated or exotic, were recorded

under the Lake Eyre Basin Rivers Assessment programme between 2011 and 2016. The

remaining seven species that had previously been recorded are exotic or translocated

species that may no longer occur in the Basin, represent taxa with uncertain taxonomic

status, or are dubious historical records. Given the aridity and lack of standing water over

long duration, this is an impressive number of native fish species, comparing well with

the Murray-Darling Basin which has 33 native freshwater species (Lintermans 2009).

The northern Murray-Darling Basin which, like the Lake Eyre Basin, also has large

sections of river that lack perennial baseflow, has only 21 native riverine species

(Balcombe et al. 2011).

The Cooper Creek catchment historically contains a total of 20 fish species, including

four exotic or translocated species (Table 4). There are also reliable anecdotal reports of

Murray cod from the Cooper (David Sternberg, personal communication.). However, this

species has not been recorded in six years of Lake Eyre Basin Rivers Assessment

monitoring, suggesting limited distribution and abundance if it is indeed present.

The Georgina-Diamantina catchment historically contains 16 fish species, including


three exotic or translocated species (Table 4). There is uncertainty, about the continued

presence of translocated silver perch and Murray-Darling golden perch in these

catchments as they have not been recorded in six years of Lake Eyre Basin Rivers

Assessment monitoring.

The Finke River has nine species of fish and no exotic or translocated species (Unmack

2001; Duguid et al. 2005; Duguid et al. 2016). The Finke River fish community is also of

interest in that it contains three species endemic to that catchment (Finke goby, Finke

River hardyhead and Finke mogurnda), probably as a result of disconnection from the

rest of the Basin (Table 4).

Twelve species of fish have been recorded in the Neales River, including one exotic

species, gambusia. Four species in this catchment have only been observed occasionally

(Welch’s grunter and Barcoo grunter) or in past surveys (silver tandan and Hyrtl's

catfish, captured in ARIDFLO surveys in the early 2000s; Costelloe et al. 2004) but not

during the Lake Eyre Basin Rivers Assessment programme.

The Macumba River, with 11 fish species, is the least studied of the Basin catchments

and, until recently, only five species were recorded there (Cockayne et al. 2012).

Another six species have now been observed in sites within the lower reaches, probably

as a result of connectivity to the Diamantina River in 2011 and 2012 (Cockayne et al.

2012).

Image 8 Hyrtl's tandan and barred grunter (at rear). Photo: M Rittner.


Table 4. Distribution of riverine fish species in the Lake Eyre Basin (updated from Unmack & Wager 2000).

Family Genus Species Common name Cooper Georgina Diamantina Finke Macumba Neales

Clupeidae Nematalosa erebi bony herring ✓ ✓ ✓ ✓ ✓ ✓

Retropinnidae Retropinna semoni Australian smelt ✓ - - - - -

Plotosidae

Neosiluroides cooperensis Cooper catfish^ ✓ - - - - -

Neosilurus hyrtlii Hyrtl's catfish ✓ ✓ ✓ ✓ ✓ ✓

Porochilus argenteus silver tandan ✓ ✓ ✓ - ✓ ✓

Atherinidae Craterocephalus centralis Finke River hardyhead^ - - - ✓ - -

Craterocephalus eyresii Lake Eyre hardyhead^ ✓ ✓ ✓ - ✓* ✓

Melanotaeniidae Melanotaenia splendida tatei desert rainbowfish^ ✓ ✓ ✓ ✓ ✓ ✓

Ambassidae Ambassis sp. desert glassfish ✓ ✓ ✓ ✓ ✓* -

Percichthyidae Macquaria ambigua Murray-Darling golden perch* - ✓ - - - -

Macquaria sp. Lake Eyre yellowbelly^ ✓ ✓ ✓ - ✓* ✓

Maccullochella peelii Murray cod† ✓ - - - - -

Terapontidae

Amniataba percoides barred grunter - ✓ ✓ ✓ ✓* ✓

Bidyanus bidyanus silver perch† - ✓ - - - -

Bidyanus welchi Welch's grunter^ ✓ ✓ ✓ - ✓* ✓*

Leiopotherapon unicolor spangled perch ✓ ✓ ✓ ✓ ✓ ✓

Scortum barcoo Barcoo grunter ✓ ✓ ✓ - * ✓

Eleotridae

Hypseleotris klunzingeri Western carp gudgeon ✓ - - - - -

Hypseleotris sp.A Midgley’s carp gudgeon ✓

Hypseleotris sp.B Lake’s carp gudgeon ✓

Mogurnda larapintae Finke mogurnda^ - - - ✓ - -

Oxyeleotris lineolatus sleepy cod* ✓ - - - - -

Gobiidae

Chlamydogobius eremius desert goby^ - - ✓ - - ✓

Chlamydogobius japalpa Finke goby^ - - - ✓ - -

Glossogobius aureus golden goby - ✓ ✓ - - -


Family Genus Species Common name Cooper Georgina Diamantina Finke Macumba Neales

Poeciliidae Gambusia holbrooki Eastern gambusia† ✓ ✓ ✓ - - ✓

Cyprinidae Carassius auratus goldfish† ✓ - - - - -

Total native species 14 13 14 9 10 11

Total translocated species 2 2

Total exotic species 2 1 1 1

^ Endemic to the Lake Eyre Basin; * translocated species; † species exotic to the Lake Eyre Basin; ✓ known distribution; * first record by Lake Eyre

Basin Rivers Assessment monitoring.


3.4.3 Endemicity and evolution

A high proportion of fish species (40%) in the Lake Eyre Basin are endemic (i.e. are

unique to the Basin). Most (90%) of these endemic species are limited to spring habitats.

In contrast, riverine fish communities in the Lake Eyre Basin Agreement Area are similar

to those of the nearby Bulloo, Barkly and Torrens river basins (Unmack 2001). Several

neighbouring regions share species with the diverse fish communities of the Basin,

including the Murray-Darling Basin (9 common species), the Burdekin catchment (8

common species), the southern Gulf of Carpentaria (10 common species) and the western

gulf of Carpentaria (9 common species) (Unmack 2001). Highly mobile species, such as

spangled perch, can exhibit low genetic variation across these catchments, suggesting

gene transfer through evolutionary and contemporary periods.

Within the Basin, the Finke River has the highest level of endemicity with three of its nine

species unique to the catchment, i.e. Finke goby, Finke mogurnda and Finke River

hardyhead. Cooper Creek has one endemic riverine species, the Cooper Creek catfish,

while the Georgina-Diamantina has none.

Recent genetic studies of Lake Eyre yellowbelly, desert rainbowfish, desert glassfish and

desert goby indicate low genetic similarity of populations between catchments of the

Basin but a high level of connectivity within Basin rivers (Huey et al. 2011; Cockayne et al.

2013; Beheregaray & Attard 2015; Mossop et al. 2015). Studies of genetic variation in

both Lake Eyre yellowbelly and desert rainbowfish, for example, show that populations

in the Cooper are isolated from those in the Georgina, Diamantina, Macumba and Neales,

suggesting a lack of contemporary connectivity via Kati Thanda – Lake Eyre amongst

these catchments (Beheregaray & Attard 2015). Similarly, desert rainbowfish from the

Finke River exhibit a large divergence from those elsewhere in the Basin, indicating long-

term isolation of the Finke and a trend towards speciation in this catchment

(Beheregaray & Attard 2015). Desert gobies also demonstrate genetic differentiation

between Basin catchments, especially in the Finke. However, for a species with seemingly

low dispersal ability, surprisingly high connectivity within catchments is apparent in the

desert goby (Mossop et al. 2015).

3.4.4 Exotic and translocated species

Fish monitoring over the last five years reveals the presence of two exotic and one

translocated fish species in the Lake Eyre Basin. Two were introduced from the northern

hemisphere, goldfish and gambusia. The other, sleepy cod, is a translocated species native

to other Australian catchments but introduced to the Cooper Creek catchment.

Goldfish

Previous studies have listed goldfish as neither common nor widespread in the Basin

(Arthington et al. 2005; Balcombe & Arthington 2009; Costello et al. 2010; Kerezsy

2010). It has been suggested that the naturally variable hydrological regimes of the

unregulated Basin rivers afford some resistance to the establishment and proliferation

of exotic fish (Costelloe et al. 2010). The lack of goldfish larvae and young juveniles

detected during periods of large floods, for example, suggests that floods could

potentially disrupt reproduction and recruitment of this species (Costelloe et al 2010).

However, comparatively high abundances of both adult and sub-adult goldfish were found


throughout the Cooper, including the Thomson, Cooper and Barcoo systems, following

the 2010-2011 wet season, with numbers subsequently diminishing rapidly in response

to prolonged drought.

Monitoring revealed that goldfish recruitment is linked to flow conditions, with

consecutive years of above average flows providing ideal conditions for population

growth. In response to natural causes, notably the variable hydrological regime, goldfish

are likely to return to lower numbers following such high recruitment. The abundance of

sub-adult goldfish in the lower Cooper also suggests that the upper and mid Cooper

may act as a source of goldfish for the lower catchment. Furthermore, goldfish

distribution is likely to be controlled by waterhole persistence, with more goldfish

occurring in areas where waterholes last for longer (i.e. upper and mid Cooper).

Gambusia

Gambusia were recorded in low numbers in sites monitored by the Lake Eyre Basin

Rivers Assessment (Cockayne et al. 2012; Sternberg et al. 2014; Mathwin et al. 2015;

Duguid et al. 2016) and appear to have minimal impact on native species in most riverine

habitats (Costelloe et al. 2010). Their persistence in riverine habitats, as well as large

populations inhabiting uncontrolled artesian bores, presents a threat to native endemic

fish of nearby spring habitats (e.g. the endangered red-finned blue-eye, Scaturiginichthys

vermeilipinnis) which may infrequently be connected to riverine habitats (McNeil et al.

2011).

Sleepy cod

Sleepy cod is a large, fish-eating gudgeon native to coastal drainages of north-eastern

Australia and the Gulf of Carpentaria. When introduced to new habitats, this species can

affect the abundance of small-bodied fish that are generalist predators through both

competition and direct predation. Consequently, sleepy cod is considered a conservation

risk to native fish species outside its natural range (Pusey et al. 2006).

Prior to 2008 sleepy cod were not recorded from the Basin. Current records, indicate that

this species has colonised many waterholes and ephemeral streams of Cooper Creek

within a decade (Sternberg & Cockayne unpublished data). Fish size data, collected over

six consecutive years (2011-2016) under the Lake Eyre Basin Rivers Assessment

programme, suggest a ‘colonising front’ of this species moving downstream with an

origin in the vicinity of Longreach (Sternberg & Cockayne unpublished data).


3.4.5 Condition assessment

Biological Condition Assessment

The condition of fish communities in waterholes monitored under the Lake Eyre Basin

Rivers Assessment programme is evaluated here according to a conceptual framework

known as the Biological Condition Gradient. This framework was initially developed in the

United States to explain observed biological responses to stressors in aquatic ecosystems

(Davies & Jackson 2006) and has since been adopted by the European Water Framework

Directive and the South Australian Environment Protection Agency and South Australian

Research and Development Institute for river condition assessment, including the Lake

Eyre Basin Rivers Assessment programme.

The Biological Condition Gradient framework provides an approach for evaluating the

response of aquatic ecosystems to stress by considering how particular ecological

‘attributes’ vary between ‘tiers’ of increasing stress that range from a ‘natural’ or

unmodified state (Tier 1) to a severely altered state (Tier 6; Figure 10). For the Basin

condition assessment, seven attributes were considered including various aspects of fish

community structure. For a complete description of these attributes and how they vary

between tiers, refer to Appendix 2.

To apply the Biological Condition Gradient framework in the Basin, fish data collected

under the Lake Eyre Basin Rivers Assessment programme were used to divide catchments

into spatial ‘ecoregions’ that represented reaches in which fish community dynamics

exhibited similar patterns (Schmarr et al. 2015). Hydro-climatic ‘phases’ were also

delineated in time – dispersal phases, boom phases and bust phases (Schmarr et al. 2015).

Specific attributes describing fish communities were then evaluated within the context of

particular ecoregions and hydro-climatic phases to generate ‘condition scores’ based on

expected responses according to the six tiers of increasing stress and degradation

(Table 5). More detailed information is provided in Appendix 2 regarding the rules used to

Figure 10 Conceptual diagram illustrating the Biological Condition Gradient framework. The diagram shows the six tiers of decreasing biological condition in relation to a gradient of increasing stress.


determine Biological Condition Gradient scores for each attribute.

In evaluating condition scores, a score of ‘3’ was adopted as a threshold of potential

concern at a site scale (Table 5). Like limits of acceptable change, thresholds of potential

concern are intended to alert managers to changes that may require a management

response. Anomalies in particular attributes that might be overlooked at a site scale were

also included in the Biological Condition Gradient rules developed for each site, and these

‘attribute thresholds of potential concern’ were set at a tier score of 5 or 6 (Appendix 2).

Condition score Level of condition

1-2 Good

2-3 Acceptable

3-4* Poor

4-5* Very poor

5-6* Dire

Table 5 Fish community condition scores based on the Biological Condition Gradient framework. * indicates scores beyond thresholds of potential concern at a site level.

Image 9 Fish sampling for the Lake Eyre Basin Rivers Assessment programme. Photo: D McNeil.

.


Overall condition

Fish communities in sampled waterholes of the Basin appear to be in good overall

condition based on the assessment of data collected between 2011 and 2016. Condition

scores mostly ranged between 1 and 3 (i.e. good to acceptable; Table 5) and were,

therefore, predominantly below the trigger value of 3 indicating a threshold of potential

concern (Figure 11).

The matter of greatest disquiet regarding fish community condition is the expanding

distribution and abundance of invasive fish species. In particular, sleepy cod have spread

from a source population in the vicinity of Longreach and become widespread and

prolific in the Queensland portion of the Cooper catchment in less than a decade. Sleepy

cod have also expanded into the South Australian portion of the Cooper Creek catchment

between 2015 and 2016. The effects of sleepy cod on native fish populations and

community condition are unlikely yet to be fully realised. Most other observed anomalies

in the abundance and diversity of native fish detected during the Lake Eyre Basin Rivers

Assessment monitoring are likely to reflect natural patterns of hydrological variability.

.

Figure 11 Average condition scores for fish communities in waterholes of each Lake Eyre Basin catchment sampled under the Lake Eyre Basin Rivers Assessment programme between 2011 and 2016 (see Table 5). Dashed line indicates threshold of potential concern.


Cooper Creek catchment

Four ecoregions were delineated in the Cooper Creek catchment; the upper Cooper,

upper-mid Cooper, lower-mid Cooper and the lower Cooper (Figure 12). Fish

communities were found to be in good (scores 1-2) to acceptable condition (scores 2-3)

over the sampling period (Figures 11 & 12; Appendix 3). The upper-mid Cooper scored

the highest condition whilst the upper Cooper, lower-mid Cooper and lower Cooper

ecoregions were all found to be in acceptable condition (Figure 12). A slight downward

trend in condition scores was apparent in the Cooper Creek over the monitoring period,

reflecting the influence of exotic and translocated fish species, especially sleepy cod

(Figure 11).

General trends in fish communities over the monitoring period were relatively similar

across the Cooper Creek catchment following the large flood in 2010 (Figure 12). After

this time, fish communities diverged between ecoregions according to the presence and

availability of different habitats in each region (Table 6; Figure 12). In particular, small-

bodied resilient species appeared to exploit the extensive aquatic habitats that were

available during boom years (2011-2012) while larger, longer-lived resilient species

dominated refuge habitats during bust years (2013-2016; Table 6). In some ecoregions

(e.g. upper-mid Cooper), this transition occurred later and was more subtle than in

others. In the lower Cooper, bust phase fish communities were also dominated by salt-

tolerant Lake Eyre hardyhead, reflecting the saline condition of persistent aquatic

habitats at this time (Table 6).

Thresholds of potential concern were triggered at a site scale in only four out of 133

samples evaluated over the sampling period, including two samples at a single site

(Figure 12; Appendix 3). These were associated with translocated and exotic species in

all cases, as follows.

• A decline in native fish diversity at Darr River in May and November 2014

comprising low numbers of native species and growing abundance of sleepy cod. It

would be beneficial to monitor this site to determine potential impacts associated

with the spread of sleepy cod.

• Disproportionately high numbers of silver tandan at Windorah Bridge in August

2011, reducing overall native fish diversity. This pattern is consistent, nevertheless,

with the boom and bust ecology of fish in Basin rivers (Balcombe & Arthington

2009). High numbers of goldfish were also present at this site and may also be of

concern. However, mass kills of this exotic species are likely during bust periods as

resources become limiting.

• An unusually depauperate fish community, with no large bodied and few resilient

species, in Cullyamurra waterhole in November 2011. Low species diversity in this

sample was caused by high levels of bony herring and high numbers of exotic

gambusia and goldfish. This community is distinct from that previously found at

Cullyamurra and more closely resembles that of an ephemeral floodplain fish

community. However, given that this event occurred during the 2010-2012 flood

and the fish community returned to that usually observed in the upper - mid

Cooper in subsequent samples, this observation may be considered an anomaly

driven by extreme hydrological variation.


Attribute thresholds of potential concern were triggered on 22 occasions in the Cooper

catchment during the monitoring period, mostly in the upper and upper-mid Cooper

ecoregions (Appendix 3). Eleven of these were triggered by the spread of sleepy cod (i.e.

samples where this translocated species had not previously been recorded) and five

were triggered by a significant increase (more than two-fold) in the abundance of sleepy

cod between consecutive sampling dates. Two thresholds of potential concern were

triggered where exotic fish species were dominant in species richness or total

abundance, while a further three were triggered by a lack of medium to small-bodied

resilient fish species in ecoregions and hydro-climatic phases in which they were

expected to be prevalent. Finally, a single threshold of potential concern was triggered

by the absence of bony herring at a site which is an unusual occurrence in the catchment

where salinity is relatively low.

Overall, the distribution and abundance of sleepy cod is the greatest concern in the

Cooper Creek catchment throughout the Lake Eyre Basin Rivers Assessment monitoring,

with range expansion indicating that this species has established a population throughout

the entire catchment. Sleepy cod were also observed to proliferate at sites once

established, particularly from 2015. The presence of this species in South Australia in

2016, especially in Coongie Lakes and Cullyamurra waterhole, provides evidence that

they are fast becoming a greater threat than initially thought.

An absence of most small to medium-bodied resilient fish at some sites in the upper

Cooper during 2014 to 2015 is also of concern, with Hyrtl's catfish the only taxon present

from this group in 2014-2015 samples. Further monitoring is required to determine

whether increased abundance of sleepy cod is having a detrimental effect upon these

native species or whether their absence is the product of drying in the region at this time,

given the more ephemeral nature of the tributaries of the upper Cooper.

Both occasions at Cullyamurra and Lake Hope where exotic taxa dominated fish

communities were associated with extremely high numbers of gambusia during the

2011 flood period, indicating that conditions at this time were conducive to population

growth of this exotic species. Given that numbers of gambusia dropped shortly

thereafter, these events are considered anomalies caused by hydro-climatic factors

which would likely occur again in similar conditions. The frequency and intensity of

these population events would beneficially be monitored in future to determine the impact

of gambusia on native fish species and the effects of boom events on source populations

of gambusia.


Table 6. Dominant fish species in monitored waterholes in the Cooper under boom and bust conditions between 2011 and 2016. Major causes of change in fish

communities are also indicated.

Ecoregion Boom Phase (2011-12) Bust Phase (2013-16) Major drivers

Upper Cooper Small-bodied, resilient species (carp gudgeon, desert rainbowfish) and species with resilient life-history and resistance to harsh conditions (bony herring)

Large-bodied resilient species (Lake Eyre yellowbelly), longer-lived resilient species (Hyrtl’s tandan) and species with resilient life-history and resistance to harsh conditions (bony herring and spangled perch)

Annual variability and persistence of habitats

Upper-mid Cooper

Large-bodied resilient species (Lake Eyre yellowbelly), longer-lived resilient species (Hyrtl’s tandan and silver tandan) and species with resilient life-history strategy and resistance to harsh conditions (bony herring) A spatial trend was observed between upstream areas, dominated by large-bodied resilient species (Lake Eyre yellowbelly), to downstream reaches dominated by species with a resilient life-history (carp gudgeons, desert rainbowfish) and species with resilient life-history and resistance to harsh conditions (bony herring)

Large-bodied resilient species (Lake Eyre yellowbelly), longer-lived resilient species (Hyrtl’s tandan) and species with resilient life-history and resistance to harsh conditions (bony herring) remained dominant Subtle changes in composition resulted in some species becoming less dominant (silver tandan) Rare taxa (Cooper Creek tandan) and species with unpredictable occurrence (Australian smelt) dominated sites on two occasions

Availability of deep waterholes

Lower-mid Cooper

Small-bodied species with a resilient life-history (desert glassfish, carp gudgeons, desert rainbowfish) and species with resilient life-history and resistance to harsh conditions (bony herring, spangled perch)

Large-bodied resilient species (Lake Eyre yellowbelly), longer-lived resilient species (Hyrtl’s tandan, silver tandan) and species with resilient life-history and resistance to harsh conditions (bony herring)

Transition from widespread ephemeral habitats to limited persistent refuges

Lower Cooper

Small-bodied species with a resilient life-history (carp gudgeons, desert rainbowfish) and species with resilient life-history and resistance to harsh conditions (bony herring and spangled perch)

Salinity tolerant taxa (Lake Eyre hardyhead) and

species with resilient life-history and resistance to harsh conditions (bony herring)

Transition from widespread ephemeral habitats to limited saline habitats


.

Figure 12 Maps showing Biological Condition Gradient scores for fish communities at waterholes sampled in the Lake Eyre Basin Cooper Creek catchment between 2011 and 2016. Shading indicates ecoregions: upper Cooper (yellow), upper mid Cooper (blue), lower mid Cooper (green) and lower Cooper (red). Samples are represented by coloured dots, with condition scores represented by colour as per the legend. Red borders around some coloured dots indicate sites where thesholds of potential concern were triggered.


Georgina-Diamantina catchments

Six ecoregions were delineated in the Georgina-Diamantina catchments; the upper

Georgina, upper-mid Georgina, the upper Georgina-Diamantina channel country, the

lower Georgina-Diamantina channel country, the Goyder and the Warburton (Figure 13).

Most fish communities were in good condition (scores 1-2) over the sampling period

(Figures 11 & 13; Appendix 3). The lower Georgina-Diamantina channel country

ecoregion had the best condition (i.e. good), while the Warburton ecoregion scored the

lowest with condition scores ranging from acceptable (scores 2-3) to good (scores 1-2)

but with some sites in poor condition (scores 3-4; Figures 11 & 13).

A small, stepped decline in condition scores was apparent in the Georgina-Diamantina

catchments from autumn 2012 (Figure 11). However, this merely reflects the addition

into the Lake Eyre Basin Rivers Assessment programme of Mungerannie Wetland, a

refuge fed by an artesian bore, which scored poorly on all occasions due to low fish

abundance and diversity and high proportions of exotic gambusia. Due to the modest

number of sites sampled in each season within the Georgina-Diamantina catchments, the

effect of the Mungerannie score on average catchment condition was disproportionately

high. With this site excluded, all average condition scores were classified as good.

Fish communities in the Georgina-Diamantina catchments are affected by a range of

spatial and geomorphological factors. Sites of similar latitude and within similar

geomorphic regions (e.g. the Mitchell Grass Downs region) tend to support similar fish

communities across separate catchments. In contrast to the dramatic temporal patterns

observed in the Cooper Creek catchment, major changes in fish communities were not

observed in most ecoregions of the Georgina-Diamantina between the boom and bust

phases (Table 7). The exception was the Warburton ecoregion, where stark changes in

hydrology associated with drying resulted in a shift from fish communities dominated by

large-bodied resilient species (e.g. Lake Eyre yellowbelly), to extremely tolerant species

(e.g. Lake Eyre hardyhead and desert goby; Table 7, Figure 13).

Thresholds of potential concern were triggered at a site scale in only five out of 115

samples evaluated over the sampling period, with three of these occurring at Mungerannie

wetland (Figure 13; Appendix 3). These were as follows:

• Reduced species richness of native fish at Ooratippra Waterhole in autumn 2014.

Given the position of this site in the upper Georgina, as well as the lack of

significant flows in the preceding year, this unusual decline in native fish diversity

may be attributed to a lack of hydrologic connection with other channels and a

lack of persistent waterholes in the vicinity; it is likely to be within the range of

natural variation for this site. Native fish species richness at the site had recovered

in autumn 2015.

• Depauperate fish community at Pandie Pandie in May 2014 comprising few

resilient species and low numbers of all but one species, Welch's grunter, which

was present in moderate abundance. The absence of Bony herring triggered this

threshold of potential concern. This species was, observed at this site only one

month earlier and its lack of detection in May probably reflects the randomness of

sampling.

• Depauperate fish communities, characterised by resistant fish species (bony

herring, spangled perch and Lake Eyre hardyhead) and high proportions of


invasive gambusia, were observed at Mungerannie Wetland in autumn 2013,

spring 2013 and spring 2014. These observations are typical for a bore-fed,

artificial wetland, and are consistently observed in other anthropogenic habitats in

the Basin, including Poonaranna Bore (Warburton River), Tepamimi Waterhole

(Eyre Creek), Old Peake Bore (Neales River) and the now decommissioned Big

Blythe Bore (Neales River). Mungarannie Wetland, and other poorly managed

bores, are of concern due to the opportunity they provide for source populations

of the exotic gambusia to persist, and possibly to spread under suitable conditions.

Nine attribute thresholds of potential concern were triggered in the Georgina-Diamantina

catchments during the monitoring period (Appendix 3). These included three occasions

in which large-bodied resilient taxa were absent where they were expected to be

prevalent, such as in the upper reaches of the Georgina-Diamantina catchments.

However, these observations are likely to reflect natural variation and are not cause for

concern.

Two attribute thresholds of potential concern were triggered by unexpected reductions

in the number of medium to small-bodied resilient fish species in Old Cork Waterhole, in

which only a single such species, Hyrtl's catfish, was observed in May 2014 and May 2015.

In April 2016, only one other species (silver tandan) had returned to this site. A broader

decline in small-bodied species throughout the upper channel country ecoregion,

involving both desert glassfish and rainbow fish, was also observed throughout the 2014-

2016 period, triggering thresholds of potential concern. These observations may be a

cause for concern and future monitoring should assess if such losses are due to low

detection rates or reflect actual species loss.


Table 7. Dominant fish species in monitored waterholes in the Georgina-Diamantina under boom and bust conditions between 2011 and 2016. Major cause

of change in fish communities are also indicated.

Ecoregion Boom Phase (2011-12) Bust Phase (2013-16) Major drivers

Upper Georgina Small-bodied species with a resilient life-history (desert rainbowfish, desert glassfish, Hyrtl’s tandan, silver tandan) and species with resilient life-history and resistance to harsh conditions (bony herring)

No major change in fish community dynamics compared to the boom phase

A diverse range of habitats support a fairly consistent community

Upper-mid Georgina Large-bodied resilient species (Lake Eyre yellowbelly), resilient catfish (Hyrtl’s tandan, silver tandan) and species with resilient life-history and resistance to harsh conditions (bony herring)

Species with resilient life history and resistance to harsh conditions (bony herring) as well as large-bodied resilient species (Lake Eyre yellowbelly). Resilient catfish (Hyrtl’s tandan, silver tandan) less dominant with drying

Availability of large waterholes

Upper Georgina- Diamantina Channel Country

Species with a resilient life-history and resistance to harsh conditions (bony herring) as well as large-bodied resilient species (Lake Eyre yellowbelly); some small-bodied species with a resilient life-history (desert rainbowfish, desert glassfish) observed towards the lower section

No major change in fish community dynamics compared to the boom phase


Lower Georgina- Diamantina Channel Country

Resilient species, such as catfish (Hyrtl’s tandan, silver tandan), as well as large-bodied resilient species (Barcoo grunter and Lake Eyre yellowbelly)

Similar to that of boom phase but with increased dominance of bony herring (a resilient life-history strategist with a resistance to harsh conditions)


Goyder Large-bodied resilient species (Lake Eyre yellowbelly), longer-lived resilient species, (silver tandan and bony herring)

Large-bodied resilient species (Lake Eyre golden perch), longer-lived resilient species, (silver tandan, Hyrtl’s tandan, bony herring), with (Hyrtl’s tandan) appearing in 2014-15; one community was also dominated by gambusia in this period


Warburton Large-bodied resilient species (Lake Eyre yellowbelly), with some resistant species (desert hardyhead) particularly in downstream areas

A more resistant community developed with drying, where most communities dominated by extremely tolerant fish (desert hardyhead, desert goby) throughout the 2014-15 period

Transition from widespread ephemeral habitats to limited saline habitats


Figure 13 Maps showing Biological Condition Gradient scores for fish communities at waterholes sampled in the Georgina Diamantina catchments between 2011 and 2016. Shading indicates ecoregions: upper Georgina (yellow), upper mid Georgina (purple), upper Georgina-Diamantina Channel Country (light blue), lower-Georgina-Diamantina Channel Country (dark blue), Goyder (green) and Warburton (red). Samples are represented by coloured dots, with condition scores represented by colour as per the legend. Red borders around some coloured dots indicate sites where thresholds of potential concern were triggered.


Finke River catchment

Two ecoregions were delineated in the Finke River catchment; the Finke tributary and the Finke

main channel (Figure 14). Most fish communities were in good (i.e. scores 1-2) to acceptable (2-3)

condition over the sampling period (Figures 11 & 14; Appendix 3). Overall condition scores

exhibited a slight decline in the Finke catchment during 2013-2014, mainly as a result of higher

scores in the lower reaches of the main channel ecoregion. However, this decline in condition is

not a cause for worry because it is associated with changes in fish abundance and diversity at two

sites (Snake Hole and Salty Snakes Tail Waterhole) where natural rises in salinity occurred in

response to drying.

Unlike other major rivers of the Basin, the Finke does not connect to Kati Thanda - Lake Eyre. As a

result, a high proportion (3 out of 9) species present in the Finke are endemic to this catchment

and the fish community is consequently distinct from the rest of the Basin. The elevation and

extent of the rocky upland catchment areas are also unique in the Basin and most of the Finke

River and its tributaries have sandy or rocky river beds which typically results in low turbidity in

persistent waterholes. Saline groundwater is also an important influence in some parts of the

catchment and many waterholes are semi-saline to saline.

While much of the Basin experienced a boom phase from 2010 to 2011 followed by a bust,

hydrologic changes in the Finke catchment were less distinctive. Consequently, fish condition

assessment was not undertaken in relation to hydro-climatic phases in this catchment. Instead,

fairly stable fish communities were observed across the Finke River catchment over the sampling

period in both ecoregions, probably reflecting the large flow events of 2010 and early 2011

followed by a long period of near continuous and reasonably predictable flow (Table 8). The

relative proximity of samples waterholes is also likely to allow mobile species, such as spangled

perch, to become widespread in this catchment while periods of higher salinities probably

facilitate the prevalence of tolerant species such as Finke River hardyhead and barred grunter in

drier periods (Table 8).

No thresholds of potential concern were triggered at a site scale within the Finke River

catchment during the sampling period and the lowest condition score recorded was 2.8. However,

five attribute thresholds of potential concern were triggered, all in the main channel ecoregion

(Appendix 3).

• A single threshold of potential concern was triggered in autumn 2013 by the 18 month

absence of Finke mogurnda at Lower Two Mile. However, this species had not previously

been observed at that site at that time, probably due to the moderate to high salinities that

are unfavourable for this species. Subsequent detection of this species at this site is thought

to be the result of river flows allowing dispersal and a temporary reduction in salinity as a

result of fresh channel flows.

Absence of Finke mogurnda from three sites during the following spring, although one of

this species had never been detected previously at one of these sites. At Snake Hole, the

water had become saline and therefore unfavourable for this species. This is probably a

natural salinity cycle in Snake Hole and not cause for concern (Duguid 2013). At the third

site (Three Mile), salinity was low and Finke mogurnda had been recorded there in the

autumn by the Northern Territory Museum (Bushblitz Survey of Henbury, May 2013). The

reason for non-detection is unclear but may reflect low abundance or behavioural patterns.

This species was caught in abundance at this site the following autumn, before connecting

flows had occurred that would have allowed migration into the waterhole.


• Continued absence of Finke mogurnda from Snake Hole the following autumn (March

2014) also triggered a threshold of potential concern. This was again due to a natural

increase in salinity at this site over a two year period without flow.

• The absence of desert glassfish at Ormiston Gorge in autumn 2013 triggered a threshold of

potential concern as the species had not been detected at this site for a period of 12 months.

However, the site has only been sampled twice under the Lake Eyre Basin Rivers Assessment

programme (autumn 2012 and autumn 2013) and this species was not detected on either

occasion. It is possible that desert glassfish are only occasionally present at this site, and that

more frequent sampling is required to establish trends in presence and absence.

Consequently, no decline in condition is indicated by the triggering of this threshold of

potential concern.

Table 8. Dominant fish species in monitored waterholes in the Finke River between 2011 and

2016. Major causes of change in fish communities are also indicated.

Eco-region Most sampling times and sites Exceptions Major drivers

Finke tributary

(upper catchment only)

Moderately stable and characterised by mobile species (desert rainbowfish and spangled perch)

In Autumn 2014, one waterhole contained a suite of small-bodied resilient species (Hyrtl’s tandan, desert rainbowfish and bony herring)

Semi to near permanent waterholes allowing colonisation opportunities for mobile species

Finke main channel refugia

Small to medium-bodied species with a resilient life-history (Hyrtl’s tandan, desert rainbowfish, desert glassfish and spangled perch) and species with resilient life-history and resistance to harsh conditions

Species with resilient life-history and resistance to harsh conditions (Finke River hardyhead and barred grunter) in 2013 and 2014 (drier periods)

Availability of permanent waterholes, short distance between waterholes for dispersal and variability in amount and salinity of groundwater inputs

Macumba River catchment

Most fish communities in the Macumba catchment were in good (i.e. scores 1-2) to acceptable (2-

3) condition throughout the sampling period (Figures 11 & 14; Appendix 3). The Macumba River

catchment, encompassing the main channel of the Macumba River and its tributaries, lacks long

term refuges (waterholes that persist for more than two years). Consequently, the fish

community relies on dispersal from the Georgina-Diamantina catchment when connecting flows

join the Macumba River to the Kallakoopah (a lower reach of the Georgina-Diamantina) north of

Kati Thanda-Lake Eyre. This favours highly mobile species such as spangled grunter and

rainbowfish. During sustained boom phases, fish with poorer dispersal capabilities may enter the

catchment from the Georgina-Diamantina.

Thresholds of potential concern were triggered at a site scale for two samples during the sampling

period, both in Murdarinna waterhole. No fish were present in this site in autumn 2014 and, in

autumn 2016, only a single species (spangled perch) was present. This site is in the upper reaches

of the Macumba catchment and persists for less than a year without flow. The absence of fish at


this site at these times reflects the lack of connectivity with downstream waterholes that might

enable dispersal of fish to this site from other populations. Consequently, these observations

appear to reflect the naturally occurring cycle of this waterhole and are not cause for concern.

Four attribute thresholds of potential concern were triggered over the sampling period in the

Macumba River catchment (Appendix 3). Three of these were associated with the absent or

depauperate fish community observed in Murdarinna waterhole associated with limited

connectivity, as described above, and not considered to be cause for concern.

The specialist Lake Eyre hardyhead was recorded within the Macumba catchment for the first

time by the sampling. This species occurred in Andarrana waterhole in autumn 2011, coinciding

with the presence of numerous other species not typically observed within this catchment,

notably smaller resilient taxa (desert glassfish and Lake Eyre hardyhead). Andaranna waterhole

is the furthest downstream site sampled within the catchment, lying 50 km upstream of where

the Macumba converges with Kallakoopah Creek. Consequently, it is not unexpected to

encounter these species here during boom periods, such as experienced prior to 2011, as

connectivity is likely to allow the dispersion of fish from the Kallakoopah and Warburton Rivers

or from unidentified downstream saline refuges in the Macumba.

Table 9. Dominant fish species in monitored waterholes in the Macumba River catchment under

boom and bust conditions between 2011 and 2016. Major causes of change in fish communities are

also indicated.

Boom Phase (2011-12) Bust Phase (2013-16) Major drivers

Dominated by mobile species with a resilient life-history (desert rainbowfish, bony herring and spangled perch)

A range of other species (Lake Eyre yellowbelly, Welch’s grunter, desert glassfish, Hyrtl’s tandan, silver tandan and desert hardyhead) were observed in the lowest Macumba sites (Andaranna and Winkies) likely migrated from the Georgina-Diamantina catchment

Dominated by mobile species with a resilient life-history (desert rainbowfish, bony herring and spangled perch)

All other species had disappeared

Low persistence of waterbodies, high intensity, low duration of hydrological events; enables species with strong migratory abilities to colonise rapidly into upstream reaches

Neales catchment

Fish communities in the Neales catchment were generally in good (i.e. scores 1-2) to acceptable

(2-3) condition over the sampling period (Figures 11 & 14; Appendix 3). Flows in this catchment

tend to be localised and of short duration, providing relatively few opportunities for fish dispersal.

Additionally, most waterholes in the catchment persist for less than two years in the absence of

flow. Algebuckina waterhole is the exception but even this may dry completely or become very

saline during extended droughts. Additional permanent artesian springs occur in this region,

especially along the Peake Creek tributary, which connect to the main channel in periods of high

flow.

Three ecoregions were identified in the Neales catchment (Table 10). The upper Neales

ecoregion encompasses the upper tributaries of the Neales River and the main channel above

Algebuckina waterhole (Figure 14). In this ecoregion, fish communities during initial boom

conditions (2011- 2012) were dominated by smaller-bodied resilient and resistant taxa until

waterholes dried in 2013 under bust conditions (Table 10). Species with strong dispersal

abilities (e.g. spangled perch and desert rainbowfish) dominated fish communities in this


ecoregion following the return of flows in 2015. Fish communities in the lower Neales ecoregion

were more stable over the sampling period and larger-bodied species were less abundant and

widespread. In the lower Peake ecoregion, including the lower reaches of the Peake Creek from

the Oodnadatta track crossing downstream to its confluence with the Neales (Figure 14), saline

groundwater influxes to waterholes had a strong influence on fish communities, which tended to

be dominated by resistant species and especially those tolerant of extreme conditions (e.g. desert

goby and Lake Eyre hardyhead; Table 10).

Three thresholds of potential concern were triggered at a site scale in the Neales

catchment over the sampling period (Figure 14; Appendix 3).

• An absence of fish in Hookeys waterhole in April 2015, despite the occurrence of recent

flows. This observation is likely to be a naturally occurring event, resulting from flows

sufficient in size to refill the waterhole but too short to allow dispersal of fish from

downstream refuges. Fish did return to this waterhole following flows in 2016.

• A depauperate fish community, lacking large-bodied resilient species (Lake Eyre yellowbelly

and Welch’s grunter), at Algebuckina waterhole in November 2011. A more resistant fish

community, lacking spangled perch and containing moderate abundances of Lake Eyre

hardyhead and desert goby, was also developing at this site. This community was

unexpected for this site during boom conditions and the result appears driven by seasonal

drying over the preceding autumn-spring. Consequently, this observation probably reflects

natural variation and is not cause for concern. Subsequent sampling in 2012 and 2013

consistently found large-bodied species and a gradual transition towards a more resistant

fish community.

• A depauperate fish community dominated by exotic gambusia in Algebuckina waterhole in

April 2015. Water levels at this site were at their lowest for the monitoring period in spring

2013, after which localised flows occurred in summer 2013-2014. In the following autumn,

significantly greater numbers of small resilient fish species were observed in Algebuckina

waterhole. A steady decline in fish abundance then occurred as water levels gradually

increased until spring 2014, after which the gambusia dominated community was observed

in autumn 2015. This chain of hydro-climatic events appears to have been conducive to

the population growth of exotic gambusia, which emerges as a concern in this catchment.

Four thresholds of potential concern were triggered in the Neales catchment over the monitoring

period (Appendix 3). These included two occasions when fish communities were dominated by

the exotic gambusia, one occasion in which large-bodied resilient fish were absent under

conditions in which they were expected Algebuckina waterhole), and one occasion in which

resilient and resistent fish species were lacking when expected (Hookeys waterhole in autumn

2015). As discussed above, only the abundance and extent of gambusia in the lower Neales and

lower Peake ecoregions appear to be cause for concern in this catchment.


Table 10. Dominant fish species in monitored waterholes in the Neales catchment under boom and bust conditions between 2011 and 2016. Major causes of

change in fish communities are also indicated.

Georgina-

Diamantina

ecoregion

Boom Phase (2011-12) Bust Phase (2013-16) Major drivers

Upper Neales Dominated by small-bodied species with resilient life-history (desert rainbowfish) and species with resilient life-history and resistance to harsh conditions (bony herring)

Comparatively stable until 2013 when most waterholes dried completely. Following flows, 2015 populations were dominated by species with strong dispersal ability (spangled perch and desert rainbowfish)

Consistent ephemeral nature of habitats support a consistent community in the absence of flow; flow periods allow dispersal by highly mobile species into these ephemeral habitats

Lower Neales Dominated by small-bodied species with a resilient life-history (desert rainbowfish) and species with resilient life-history and resistance to harsh conditions (bony herring)

Dominated by species observed during the boom period (desert rainbowfish and bony herring), until spring 2013 when the fish community transitioned into that which resembles a more resistant community, dominated by salt-tolerant species such as desert hardyhead, desert goby and eastern gambusia also contributing to the structure of the community

Availability of large waterholes

Peake Prior to monitoring in 2010 the lower Peake fish community was dominated by small-bodied species with a resilient life-history (desert rainbowfish) and species with resilient life-history and resistance to harsh conditions (bony herring). The presence of these communities was short lived, with some communities rapidly transitioning toward a more resistant community (desert hardyhead, desert goby) with eastern gambusia also driving some communities in autumn 2011. Several resilient communities were observed prior to the end of the boom period (desert rainbowfish and bony herring)

Fish communitues remained relatively stable, with resistant communities prevalent throughout (Lake Eyre hardyhead and desert goby); the exception was Warrarawoona waterhole, which dried and refilled more than once, with a corresponding return to a resilient fish community as local flow refilled the waterhole (desert rainbowfish and bony herring)

Annual variability and persistence of habitats and increased salinity during drying periods


.

Figure 14 Maps showing Biological Condition Gradient scores for fish communities at waterholes sampled in the Finke, Macumba and Neales catchments between 2011 and 2016. Shading indicates ecoregions: Finke Tributary and Macumba (yellow), upper Neales, Finke main channel (blue), lower Neales, Palmer (green) and lower Finke (red). Samples are represented by coloured dots, with condition scores represented by colour as per the legend. Red borders around some coloured dots indicate sites where thresholds of potential concern were triggered.


3.4.6 Coongie Lakes

The current limit of acceptable change set for fish in the Coongie Lakes site states that there

should be: “No less than eight of 13 native species recorded from any three of five comprehensive

sampling events (assuming seasonal sampling) from the main branch and northwest branch, from

the Queensland border downstream to Coongie Lakes and Embarka Swamp including

Cullyamurra waterhole” (Butcher & Hale 2011).

This limit of acceptable change was informed by data from Puckridge et al. (2010) which

indicated that 13 species of native fish had been recorded from the site and noted that most of

these species are commonly observed in the upper reaches of the site upstream from Coongie

Lakes. Because of incomplete knowledge of fish distributions across the site, this limit of

acceptable change was only set for the upstream section of the main channel and northwest

branch from Embarka Swamp and Coongie Lakes upstream to the Queensland border. The

maximum acceptable level of change was selected on the basis of expert opinion with

acknowledgement that this limit would likely require refinement as ecological understanding

increased through further data collection under the Lake Eyre Basin Rivers Assessment

programme (Butcher & Hale 2011).

The Lake Eyre Basin Rivers Assessment programme sampling between 2008 and 2016 found

eight or more native fish species in Coongie Lake sites on eight occasions (Table 11). If five

consecutive sampling events are considered, as stated in the original limit of acceptable change,

this threshold was exceeded on the four most recent sampling dates (Table 11), although it

should be noted that only one or two sites (Coongie inflow and Cullyamurra waterhole) were

sampled on the last six events.

A more refined approach to detecting unacceptable changes in fish communities upstream of

Coongie Lakes can now be developed using the rules defined in the Biological Condition Gradient

framework for the Cooper Creek catchment (see Section 3.4.5). The single site monitored in the

ecoregion of the Coongie Lakes (Coongie inlet in the lower-mid Cooper; Figure 13) was found to

be in either good or acceptable condition throughout the six years of the Lake Eyre Basin Rivers

Assessment monitoring . The recent appearance of Sleepy cod emerges as a potential concern,

because this exotic predator may disrupt food web dynamics in aquatic ecosystems and influence

the abundance and diversity of native fish. The Biological Condition Gradient approach is more

sensitive to such changes than the current limit of acceptable change, as it assesses the condition

of fish communities relative to the expected abundance and diversity in any given hydro-climatic

period. It would be beneficial for at least two sites in this ecoregion to be monitored in the future

to better understand changes in fish communities in the Coongie Lakes region.


Table 11. Number of fish species captured and numbers of sites surveyed in comprehensive sampling events from the Queensland border downstream to Coongie Lakes and Embarka Swamp.

Year Season Number of Species

Number of sites

2008 Autumn 12 1

2009 Autumn 10 2

2010 Spring 10 2

2011 Autumn 11 6

Spring 10 6

2012 Autumn 12 11

Spring 5 1

2013 Autumn 7 2

Spring 6 1

2014 Autumn 7 2

Spring 8 1

2015 Autumn 11 2

2016 Autumn 7 2


3.5 Waterbirds

3.5.1 Key messages

• Slight increases in the numbers of waterbirds and the number of species was apparent

across the Lake Eyre Basin over 33 years of surveys. Increased abundances in some

waterbird groups (piscivores and herbivores) and some species were also apparent. In

contrast, significant declines in total numbers and the abundance of many species were

apparent over the same period in the Murray-Darling Basin.

• The only long-term declines in waterbird abundances detected in the Basin were for

shorebirds at three wetlands (Goyders Lagoon, Lower Cooper and Lake Yamma Yamma).

There is increasing evidence for decline of migratory shorebirds in Australia, affected by

changes to habitats in their flyways and within Australia. Herbivorous waterbirds on

Lake Katherine and brolgas also showed declines in the Georgina-Diamantina catchment.

• A total of 46 waterbird species was observed in the Basin between 1983 and 2015.

Ducks tend to be the most abundant group, followed by herbivores, piscivores,

shorebirds and large wading birds.

• Waterbird numbers and diversity are highly variable at the scale of the Basin, at

catchments and at individual wetlands, largely reflecting boom and bust ecology and the

consequential variability in streamflow and wetland water levels. In general, more

waterbirds and waterbird species occurred in the Cooper Creek catchment than in the

Georgina-Diamantina catchment.

• Waterbirds were surveyed across the Coongie Lakes region (Cooper Catchment) in

November 2008 during widespread drought conditions in the Basin. High numbers of

waterbirds (almost 60 000) and waterbird species (about 45) were present at this time,

including around 2% of the total populations of red-necked avocet and pink-eared duck;

these results support the continued recognition of this site as internationally significant.

Lake Galilee (Cooper Catchment) was the most important of the wetlands assessed

through the Eastern Waterbird Aerial Survey (1983-2015) with respect to waterbird

abundance, averaging around 35 000 waterbirds a year during wet periods.

3.5.2 Overview

Waterbirds have been surveyed within ten wetlands in the catchments of the Cooper (Lower

Cooper, Lake Dunn, Lake Galilee, Lake Hope and Lake Yamma Yamma) and Diamantina-Georgina

(Goyders Lagoon, Lake Katherine, Lake Mumberry, Lake Phillippi and Lake Torquinnie) every

spring since 1983 as part of the Eastern Aerial Waterbird Survey (Figure 15 & Table 12). During

this period, a total of 46 waterbird species has been observed in the Lake Eyre Basin (Appendix 4)

with an average of 37 species recorded each year. At a catchment scale, fewer species are

generally recorded with an average of 32 species per year observed in the Cooper Creek

catchment and 28 species per year in the Georgina-Diamantina. The number of waterbird species

varies considerably between years, however, with greater variability observed at a catchment

scale than at the Basin scale (Figure 16).


Figure 15 Aerial surveys of the Georgina-Diamantina River (blue) and Cooper Creek (purple) and the ten key wetlands (listed in below table) surveyed for waterbirds annually, 1983-2015, across the Lake Eyre Basin. Location of seven aerial survey bands (each 30 kilometres wide), covering eastern Australia, and coverage of the Lake Eyre Basin, with the major wetlands and river systems. All wetlands greater than 1ha were surveyed in each survey band (Kingsford 2016).


Table 12. Ten key wetlands surveyed for waterbirds annually (Kingsford, R 2016). Site Catchment State

Lower Cooper (CP) Cooper Creek South Australia

Lake Dunn (LD) Cooper Creek Queensland

Lake Galilee (LG) Cooper Creek Queensland

Lake Hope (LH) Cooper Creek Queensland

Lake Yamma Yamma (LY) Cooper Creek Queensland

Goyders Lagoon (GL) Georgina-Diamantina South Australia

Lake Katherine (LK) Georgina-Diamantina Queensland

Lake Mumberry (MU) Georgina-Diamantina Queensland

Lake Phillippi (LP) Georgina-Diamantina Queensland

Lake Torquinnie (LD) Georgina-Diamantina Queensland

The total number of waterbirds is also highly variable between years (Figure 16). High numbers

typically occur at times of high streamflow, reflecting widespread inundation and habitat

availability (Costelloe et al. 2005). Waterbird numbers tend to be lower on average in the

Georgina-Diamantina catchment (about 33 000) than in the Cooper Creek catchment (about

65 500).

Ducks were the most abundant functional group recorded at both the Basin and catchment scale

between 1983 and 2015, followed by herbivores, piscivores, shorebirds and large wading birds

(Figure 16). From 1983 to 2015, reflecting overall abundances, there were fewer numbers of

waterbirds in each of the functional groups in the Georgina-Diamantina than in the Cooper

Creek catchment. Waterbird abundances (total and of the functional groups) were more

variable between the years in the Georgina-Diamantina catchment.

Waterbird abundance and diversity also varied considerably within individual wetlands,

although the relative proportions of different suites of birds within each wetland tend to be

similar over time at this scale (Figure 17). Lake Galilee was by far the most important wetland

assessed through the Eastern Waterbird Aerial Survey in the Basin (the survey does not assess

Coongie Lakes) with respect to waterbird abundance, with an average of almost 35 000

waterbirds observed annually during wet periods (Figure 17). During the survey period, some

wetlands were dry for long durations and did not support any waterbirds.

.


. Figure 16 Estimates of abundance of waterbirds during annual aerial surveys across eastern Australia over 33 years (1983-2015) in the Lake Eyre Basin (a); the Georgina-Diamantina catchment (b); and the Cooper Creek catchment (c); showing: species richness (dashed line), total abundance (grey fill) and abundances of each of the five functional groups (ducks, red), herbivores (green), large wading birds (purple), piscivores (light blue), and shorebirds (orange).


.

Figure17a. Estimates of waterbirds during annual aerial surveys across eastern Australia over 33 years (1983-2015) for each of the five wetlands surveyed in the Georgina-Diamantina, showing: species richness (dashed line), total abundance (grey fill) and abundances of each of the five functional groups (ducks, red), herbivores (green), large wading birds (purple), piscivores (light blue), and shorebirds (orange) for the five wetlands: Lake Katherine (LK), Lake Philipi (LP), Lake Mumberry (MU), Lake Torquinnie (LT) and Goyders Lagoon (GL). Note that these estimates are not total counts, as aerial survey bands sometimes do not include entire wetlands.

.

Figure 17b. Estimates of waterbird communities during annual aerial surveys across eastern Australia over 33 years (1983-2015) for each of the five wetlands surveyed in the Cooper Creek Catchments, showing: species richness (dashed line), total abundance (grey fill) and abundances of each of the five functional groups (ducks, red), herbivores (green), large wading birds (purple), piscivores (light blue), and shorebirds (orange) for the five wetlands: Lake Galilee (LG), Lake Dunn (LD), Lake Yamma Yamma (LY), Lake Hope (LH) and Lower Cooper Lakes (CP). Note that these estimates are not total counts, as aerial survey bands sometimes do not include entire wetlands.


3.5.3 Temporal trends

Long-term trends in total waterbird numbers, numbers of species and the abundances of

waterbird functional groups were investigated for the both the Lake Eyre Basin and the

neighbouring Murray-Darling Basin. For the Lake Eyre Basin, only 15 out of 91 identified

trends were found to be statistically significant and, of these, only four were negative. All

of these negative trends involved reductions in the abundance of shorebirds at three

wetlands (Goyders Lagoon, Lower Cooper and Lake Yamma Yamma), consistent with

evidence of long-term declines in shorebird abundance across Australia (Nebel et al.

2008; Clemens et al. 2016).

Across the Basin, slight increases in total waterbird numbers (an average annual gain of

0.76%) and the number of waterbird species were apparent between 1983 and 2015. At a

catchment-scale, neither total waterbird numbers nor numbers of species exhibited

significant long-term trends in either the Cooper or Georgina-Diamantina catchments,

although a significant increase in the abundance of piscivores was detected in the Cooper

Creek catchment (an average annual gain of 1.10%). In contrast, observations of

waterbird numbers in the Murray-Darling Basin indicate an average annual decline of

3.93% and a 72% decline in total waterbird numbers over the 33 year period. Declines

were particularly severe in the Murray-Darling Basin amongst ducks and shorebirds.

At the wetland scale, positive long-term trends were detected for the number of species

(average increase of 1.05) and total number of waterbirds (average increase of 2.86) in

Lake Hope and number of species (0.52) in Lake Katherine. The number of herbivores

also increased over the survey period in Goyders Lagoon (1.64) and Lake Hope (3.07)

while the number of piscivores grew in Lake Dunn (1.34) and Lake Hope (3.83; Figure

18).

Long-term trends in the abundance of particular waterbird species in the Basin were also

investigated. A decline was only detected in one species (brolga) and this only occurred

within the Georgina-Diamantina catchment. At a Basin scale, three species (pied

cormorants, Pacific black duck and an unidentified tern species) increased in abundance

over the survey period while three species (pied cormorant, little pied cormorants and

large waders) exhibited increases in the Georgina-Diamantina catchment, and four

species (pied cormorants, royal spoonbills, brolgas and terns) in the Cooper Creek

catchment. Interestingly, two of these species (Pacific black duck and little pied

cormorants) exhibited significant declines over the same period in the Murray-Darling

Basin.


Figure 18 Mean (± 95% confidence limits) annual trends, as a percentage of average abundance, for different waterbirds (total abundance, species richness and abundances) of the five functional groups (ducks , herbivores, large wading birds , piscivores, shorebirds), estimated during annual aerial surveys across eastern Australia over 33 years (1983-2015) for a) five wetlands within the Georgina-Diamantina river catchment (Lake Katherine (LK), Lake Philipi (LP), Lake Mumberry (MU), Lake Torquinnie (LT) and Goyders Lagoon (GL)), and for b) five wetlands within the Cooper Creek catchment (Lake Galilee (LG), Lake Dunn (LD), Lake Yamma Yamma (LY), Lake Hope (LH), Lower Cooper Lakes (CP)). Note that these estimates are not total counts as aerial survey bands sometimes do not include entire wetlands.


3.5.4 Coongie Lakes

Waterbirds in 21 wetlands in the Coongie Lakes Region of the Innamincka Regional

Reserve were surveyed in November 2008 (Kingsford et al. 2012) during a period of

widespread drought in the Lake Eyre Basin and Murray-Darling Basin. During this survey,

over 58 000 waterbirds were recorded representing at least 45 species (Appendix 5).

Overall, ducks were the most abundant group observed followed by piscivores,

shorebirds and large wading birds (Figure 19). Waterbird numbers varied considerably

between individual wetlands with larger lakes supporting higher numbers and more

species of waterbirds.

The results of this survey indicate that Coongie Lakes is likely to meet the waterfowl

abundance criterion for listing as a Ramsar site (because it regularly supports 20 000 or

more waterfowl), even though the site was not originally listed under this criterion

(Butcher & Hale 2011). Coongie Lakes is also considered internationally significant in

that it regularly supports 1% of the individuals of one species or subspecies of waterbird

(Butcher & Hale 2011). In the 2008 survey, 2 521 red-necked avocets and 21 670 pink-

eared ducks were recorded in the Coongie Lakes region, representing just over 2% of the

total estimated populations of each of these species.

Figure 19 Total counts of waterbirds on the Coongie Lakes system during aerial surveys in 2008, separated into functional groups.

Documents

3. Current status - DCQ · Draft Lake Eyre Basin State of the Basin Condition Assessment 2016 Report: for public consultation 18 3. Current status 3.1 Introduction This chapter presents