Marine and Freshwater Research Marine and Freshwater Research Society
Advances in the aquatic sciences

Ecological roles and threats to aquatic refugia in arid landscapes: dryland river waterholes

Fran Sheldon A B , Stuart E. Bunn A , Jane M. Hughes A , Angela H. Arthington A , Stephen R. Balcombe A and Christine S. Fellows A

A Australian Rivers Institute, Griffith University, Nathan, Qld 4111, Australia.

B Corresponding author. Email:

Marine and Freshwater Research 61(8) 885-895
Submitted: 23 September 2009  Accepted: 15 April 2010   Published: 13 August 2010


Dryland rivers are renowned for their periods of ‘boom’ related to the episodic floods that extend over vast floodplains and fuel incredible production, and periods of ‘bust’ where the extensive channel network is restricted to the permanent refugial waterholes. Many of these river systems are unregulated by dams but are under increasing pressure, especially from water abstraction and overland flow interception for agriculture and mining. Although some aquatic organisms with desiccation-resistant life stages can utilise ephemeral floodplain habitats, the larger river waterholes represent the only permanent aquatic habitat during extended periods of low or no flow. These waterholes act as aquatic refugia in an otherwise terrestrial landscape. Variable patterns of connection and disconnection in space and time are a fundamental driver of diversity and function in these dryland river systems, and are vital for dispersal and the maintenance of diverse populations, generate the spatial and temporal variability in assemblage structure for a range of different organisms and fuel the productivity that sustains higher trophic levels. Changes to natural patterns of connection and disconnection of refugial waterholes, owing to water-resource development or climate change, will threaten their persistence and diminish their functional capacity to act as aquatic refugia.


Amoros C.Bornette G.2002Connectivity and biocomplexity in waterbodies of riverine floodplains.Freshwater Biology47761776doi:10.1046/J.1365-2427.2002.00905.X

Andrén H.1996Population responses to habitat fragmentation: statistical power and the random sample hypothesis.Oikos76235242doi:10.2307/3546195

Arthington A. H.Balcombe S. R.Wilson G. A.Thoms M. C.Marshall J. C.2005Spatial and temporal variation in fish assemblage structure in isolated waterholes during the 2001 dry season of an arid-zone floodplain river, Cooper Creek, Australia.Marine and Freshwater Research562535doi:10.1071/MF04111

Arthington A. H.Olden J. D.Balcombe S. R.Thoms M. C.2010Interacting and hierarchical factors explain fish assemblage turnover and quality of waterholes as refugia in Cooper Creek.Marine and Freshwater Research61842856doi:10.1071/MF09096

Balcombe S. R.Arthington A. H.2009Temporal changes in fish abundance in response to hydrological variability in a dryland floodplain river.Marine and Freshwater Research60146159doi:10.1071/MF08118

Balcombe S. R.Bunn S. E.McKenzie-Smith F. J.Davies P. M.2005Variability of fish diets between dry and flood periods in an arid zone floodplain river.Journal of Fish Biology6715521567doi:10.1111/J.1095-8649.2005.00858.X

Balcombe S. R.Bunn S. E.Arthington A. H.Fawcett J. H.McKenzie-Smith F. al.2007Fish larvae, growth and biomass relationships in an Australian arid zone river: links between floodplains and waterholes.Freshwater Biology5223852398doi:10.1111/J.1365-2427.2007.01855.X

Bornette G.Amoros C.Lamouroux N.1998Aquatic plant diversity in riverine wetlands: the role of connectivity.Freshwater Biology39267283doi:10.1046/J.1365-2427.1998.00273.X

Boulton A. J.Lloyd L. N.1992Flooding frequency and invertebrate emergence from dry floodplain sediments of the River Murray, Australia.Regulated Rivers: Research and Management7137151doi:10.1002/RRR.3450070203

Breen C.1991Are intermittently flooded wetlands of arid environments important conservation sites?Madoqua176165

Bunn S. E.Arthington A. H.2002Basic principles and consequences of altered hydrological regimes for aquatic biodiversity.Environmental Management30492507

Bunn S. E., and Davies P. M. (1999). Aquatic food webs in turbid, arid zone rivers: preliminary data from Cooper Creek, Queensland. In ‘Free-Flowing River: The Ecology of the Paroo River’. (Ed. R. T. Kingsford.) pp. 67–76. (New South Wales National Parks and Wildlife Service: Sydney.)

Bunn S. E.Davies P. M.Winning M.2003Sources of organic carbon supporting the food web of an arid zone floodplain river.Freshwater Biology48619635doi:10.1046/J.1365-2427.2003.01031.X

Bunn S. E., Balcombe S. R., Davies P. M., Fellows C. S., and McKenzie-Smith F. J. (2006a). Aquatic productivity and food webs of desert river ecosystems. In ‘Ecology of Desert Rivers’. (Ed. R. T. Kingsford.) pp. 76–99. (Cambridge University Press: Cambridge, UK.)

Bunn S. E.Thoms M. C.Hamilton S. K.Capon S. J.2006bFlow variability in dryland rivers: boom, bust and the bits in between.River Research and Applications22179186doi:10.1002/RRA.904

Burford M.Cook A.Fellows C. S.Balcombe S. R.Bunn S. E.2008Sources of carbon fuelling production in an arid floodplain river.Marine and Freshwater Research59224234doi:10.1071/MF07159

Capon S. J.2003Plant community responses to wetting and drying in a large arid floodplain.River Research and Applications19509520doi:10.1002/RRA.730

Carini G.Hughes J. M.2004Population structure of Macrobrachium australiense (Decapoda: Palaemonidae) in Western Queensland, Australia: the role of contemporary and historical processes.Heredity93350363doi:10.1038/SJ.HDY.6800510

Carini G.Hughes J. M.2006Population genetic structure and phylogeography of an endangered freshwater snail, Notopala sublineata (Gastropoda: Viviparidae) in Western Queensland, Australia.Biological Journal of the Linnean Society. Linnean Society of London88116doi:10.1111/J.1095-8312.2006.00594.X

Carini G.Hughes J. M.Bunn S. E.2006The role of waterholes as ‘refugia’ in sustaining genetic diversity and variation of two freshwater species in dryland river systems (Western Queensland, Australia).Freshwater Biology5114341446doi:10.1111/J.1365-2427.2006.01585.X

Cook B. D.Bunn S. E.Hughes J. M.2002Genetic structure and dispersal of Macrobrachium australiense (Decapoda: Palaemonidae) in Western Queensland, Australia.Freshwater Biology4720982112doi:10.1046/J.1365-2427.2002.00953.X

Cooper S.Barmuta L.Sarnelle O.Kratz K.Diehl S.1997Quantifying spatial heterogeneity in streams.Journal of the North American Benthological Society16174188doi:10.2307/1468250

Davies B. R., Thoms M. C., Walker K. F., O’Keefe J. H., and Gore J. A. (1994). Dryland rivers: their ecology, conservation and management. In ‘The Rivers Handbook. Vol. 2’. (Eds P. Calow and G. E. Petts.) pp. 484–511. (Blackwell Scientific: Oxford, UK.)

Davis L., Thoms M. C., Fellows C. S., and Bunn S. E. (2002). Physical and ecological associations in dryland refugia: waterholes of the Cooper Creek, Australia. In ‘The Structure, Function and Management Implications of Fluvial Sedimentary Systems’. (Eds F. J. Dyer, M. C. Thoms and J. M. Olley.) pp. 77–84. Publication No. 276. (IAHS Press: Wallingford, UK.)

Dudgeon D.1996The influence of refugia on predation impacts in a Hong Kong stream.Archiv für Hydrobiologie138145159

Dynesius M.Nilsson C.1994Fragmentation and flow regulation of river systems in the northern third of the world.Science266753762

Fellows C. S.Bunn S. E.Sheldon F.Beard N. J.2009Benthic metabolism in two turbid dryland rivers.Freshwater Biology54236253doi:10.1111/J.1365-2427.2008.02104.X

Gustafson E. J.Gardner R. H.1996The effect of landscape heterogeneity on the probability of patch colonisation.Ecology7794107doi:10.2307/2265659

Hamilton S. K.Bunn S. E.Thoms M. C.Marshall J. C.2005Persistence of aquatic refugia between flow pulses in a dryland river system (Cooper Creek, Australia).Limnology and Oceanography50743754

Heiler G.Hein T.Schiemer F.1995Hydrological connectivity and flood pulses as the central aspects for the integrity of a river-floodplain system.Regulated Rivers: Research and Management11351361

Holmquist J. G.1998Permeability of patch boundaries to benthic invertebrates: influences of boundary contrast, light level, and faunal density and mobility.Oikos81558566doi:10.2307/3546776

Huey J. A.Hughes J. M.Baker A. M.2006Patterns of gene flow in two species of eel-tailed catfish, Neosilurus hyrtlii and Porochilus argenteus (Siluriformes: Plotosidae), in western Queensland's dryland rivers.Biological Journal of the Linnean Society. Linnean Society of London87457467doi:10.1111/J.1095-8312.2006.00590.X

Hughes J. M.Hillyer M. J.2003Patterns of connectivity among populations of Cherax destructor (Decapoda: Parastacidae) in western Queensland, Australia.Marine and Freshwater Research54587596

Hughes J. M.Hillyer M. J.2006Mitochondrial DNA and allozymes reveal high dispersal abilities and historical movement across drainage boundaries in two species of freshwater fishes from inland rivers in Queensland, Australia.Journal of Fish Biology68Suppl. B270291

Hughes J. M.Bunn S. E.Kingston D. M.Hurwood D. A.1995Genetic differentiation and dispersal among populations of Paratya australiensis (Atyidae) in rainforest streams in south-east Queensland, Australia.Journal of the North American Benthological Society14158173doi:10.2307/1467731

Hughes J. M.Baker A. M.Bartlett C.Bunn S. E.Goudkamp al.2004Past and present patterns of connectivity among populations of four cryptic species of freshwater mussels Velesunio spp. (Hyriidae) in central Australia.Molecular Ecology1331973212doi:10.1111/J.1365-294X.2004.02305.X

Jackson J. K.Resh V. J.1992Variation in genetic structure among populations of the caddisfly Helicopsyche borealis from three streams in northern California, USA.Freshwater Biology272942doi:10.1111/J.1365-2427.1992.TB00520.X

Jenkins K. M.Boulton A. J.2003Connectivity in a dryland river: short-term aquatic microinvertebrate recruitment following floodplain inundation.Ecology8427082723doi:10.1890/02-0326

Johnson B. L.Knights B. C.Barko J. W.Gaugush R. F.Soballe D. al.1998Estimating flow rates to optimise winter habitat for centrarchid fish in Mississippi River (USA) backwaters.Regulated Rivers: Research and Management14499510doi:10.1002/(SICI)1099-1646(1998110)14:6<499::AID-RRR516>3.0.CO;2-I

Junk W. J.Bayley P. B.Sparks R. E.1989The flood pulse concept in river-floodplain systems.Canadian Special Publications of Fisheries and Aquatic Sciences106110127

Kennard M. J. (1995). Factors influencing freshwater fish assemblages in floodplain lagoons of the Normanby River, Cape York Peninsula: a large subtropical river. M.Sc. Thesis, Griffith University, Brisbane, Australia.

Kingsford R. T.2000aProtecting rivers in arid regions or pumping them dry?Hydrobiologia427111

Kingsford R. T.2000bEcological impacts of dams, water diversions and river management on floodplain wetlands in Australia.Austral Ecology25109127

Kingsford R. T. (2006). Changing desert rivers. In ‘Ecology of Desert Rivers’. (Ed. R. T. Kingsford.) pp. 336–345. (Cambridge University Press: Cambridge, UK.)

Kingsford R. T., and Thompson J. R. (2006). Desert or dryland rivers of the world: an introduction. In ‘Ecology of Desert Rivers’. (Ed. R. T. Kingsford.) pp. 3–10. (Cambridge University Press: Cambridge, UK.)

Kingsford R. T.Roshier D. A.Porter J. L.2010Australian waterbirds – time and space travellers in dynamic desert landscapes.Marine and Freshwater Research61875884

Kingsford R. T.Boulton A. J.Puckridge J. T.1998Challenges in managing dryland rivers crossing political boundaries: lessons from Cooper Creek and the Paroo River, central Australia.Aquatic Conservation: Marine & Freshwater Ecosystems8361378doi:10.1002/(SICI)1099-0755(199805/06)8:3<361::AID-AQC294>3.0.CO;2-V

Kingsford R. T.Curtin A. L.Porter J. L.1999Water flows on Cooper Creek determine ‘boom’ and ‘bust’ periods for waterbirds.Biological Conservation88231248doi:10.1016/S0006-3207(98)00098-6

Knighton A. D.Nanson G. C.1994Waterholes and their significance in the anastomosing channel system of the Cooper Creek, Australia.Geomorphology9311324doi:10.1016/0169-555X(94)90052-3

Lancaster J.Belyea L. R.1997Nested hierarchies and scale-dependence of mechanisms of flow refugium use.Journal of the North American Benthological Society16221238doi:10.2307/1468253

Larned S. T.Datry T.Arscott D. B.Tockner K.2010Emerging concepts in temporary-river ecology.Freshwater Biology55717738doi:10.1111/J.1365-2427.2009.02322.X

Leigh C.Sheldon F.2008Hydrological changes and ecological impacts associated with water resource development in large floodplain rivers in the Australian tropics.River Research and Applications2412511270

Leigh C.Sheldon F.Kingsford R. T.Arthington A. H.2010Sequential floods drive ‘booms’ and wetland persistence in dryland rivers: a synthesis.Marine and Freshwater Research61896908

Lemly D.Kingsford R. T.Thompson J. R.2000Irrigated agriculture and wildlife conservation: conflict on a global scale.Environmental Management25485512doi:10.1007/S002679910039

Loreau M.2000Biodiversity and ecosystem functioning: recent theoretical advances.Oikos91317doi:10.1034/J.1600-0706.2000.910101.X

Loutit R.1991Western flowing ephemeral rivers and their importance to wetlands in Namibia.Madoqua17135140

Lundberg J.Moberg F.2003Mobile link organisms and ecosystem functioning: implications for ecosystem resilience and management.Ecosystems68798

Lutton S.Sheldon F.Bunn S. E.2010Morphological characteristics of on-farm water storages and their similarity to natural water bodies in the Border Rivers Catchment, Australia.Aquatic Conservation: Marine & Freshwater Ecosystems204757

Lynch R. J.Bunn S. E.Catterall C. P.2002Adult aquatic insects: potential contributors to riparian food webs in Australia’s wet–dry tropics.Austral Ecology27515526

Magalhães M. F.Beja P.Schlosser I. J.Collares-Pereira M. J.2007Effects of multi-year droughts on fish assemblages of seasonally drying Mediterranean streams.Freshwater Biology5214941510doi:10.1111/J.1365-2427.2007.01781.X

Marshall J. C.Sheldon F.Thoms M. C.Choy S.2006The macroinvertebrate fauna of an Australian dryland river: spatial and temporal patterns and environmental relationships.Marine and Freshwater Research576174doi:10.1071/MF05021

McGregor G. B.Marshall J. C.Thoms M. C.2006Spatial and temporal variation in algal-assemblage structure in isolated dryland river waterholes, Cooper Creek and Warrego River, Australia.Marine and Freshwater Research57453466doi:10.1071/MF05128

McMahon T. A.Finlayson B. L.2003Droughts and anti-droughts: the low flow hydrology of Australian rivers.Freshwater Biology4811471160doi:10.1046/J.1365-2427.2003.01098.X

Medeiros S. E. F.Arthington A. H.2008The importance of zooplankton in the diets of three native fish species in floodplain waterholes of a dryland river, the Macintyre River, Australia.Hydrobiologia6141931doi:10.1007/S10750-008-9533-7

Morton S. J., Short J., and Baker R. D. (1995). Refugia for biological diversity in arid and semi-arid Australia. Biodiversity Series, Paper No. 4. Report to the Biodiversity Unit of the Department of Environment, Sport and Territories, Canberra.

Nekola J. C.1999Paleorefugia and neorefugia: the influence of colonisation history on community pattern and process.Ecology8024592473doi:10.1890/0012-9658(1999)080[2459:PANTIO]2.0.CO;2

Poff N. L.1997Landscape filters and species traits: towards mechanistic understanding and prediction in stream ecology.Journal of the North American Benthological Society16391409doi:10.2307/1468026

Puckridge J. T. (1999). The role of hydrology in the ecology of Cooper Creek, South Australia. Ph.D. Thesis, University of Adelaide.

Puckridge J. T.Sheldon F.Walker K. F.Boulton A. J.1998Flow variability and the ecology of large rivers.Marine and Freshwater Research495572doi:10.1071/MF94161

Puckridge J. T., Reid J. R., Sheldon F., and Baker S. (1999). Biological survey of the Lower Diamantina floodplain, November 1993, Final Report. South Australian Department of Environment and Planning, the Australian Heritage Commission, and the Conservation Council of South Australia, Adelaide.

Puckridge J. T.Walker K. F.Costelloe J. F.2000Hydrological persistence and the ecology of dryland rivers.Regulated Rivers: Research and Management16385402doi:10.1002/1099-1646(200009/10)16:5<385::AID-RRR592>3.0.CO;2-W

Rempel L. L.Richardson J. S.Healey M. C.1999Flow refugia for benthic macroinvertebrates during flooding of a large river.Journal of the North American Benthological Society183448doi:10.2307/1468007

Roshier D.Doerr V.Doerr E.2008Animal movement in dynamic landscapes: interaction between behavioural strategies and resource distributions.Oecologia156465477doi:10.1007/S00442-008-0987-0

Sedell J. R.Reeves G. H.Hauer F. R.Stanford J. A.Hawkins C. P.1990Role of refugia in recovery from disturbances: modern fragmented and disconnected river systems.Environmental Management14711724doi:10.1007/BF02394720

Sheldon F.Fellows C. S.2010Temporal and spatial variability of water quality and water chemistry in two Australian dryland rivers.Marine and Freshwater Research61864874doi:10.1071/MF09289

Sheldon F.Puckridge J. T.1998Macroinvertebrate assemblages of Goyder Lagoon, Diamantina River, South Australia.Transactions of the Royal Society of South Australia1221731

Sheldon F.Thoms M. C.2006Relationships between flow variability and invertebrate community composition: data from four Australian dryland rivers.River Research and Applications22219238

Sheldon F.Boulton A. J.Puckridge J. T.2002Conservation value of variable connection: aquatic invertebrate assemblages of channel and floodplain habitats of a central Australian arid-zone river, Cooper Creek.Biological Conservation1031331doi:10.1016/S0006-3207(01)00111-2

Slatkin M.1985Gene flow in natural populations.Annual Review of Ecology and Systematics16393430doi:10.1146/ANNUREV.ECOLSYS.16.1.393

Stanley E. H.Fisher S. G.Grimm N. B.1997Ecosystem expansion and contraction in streams.BioScience47427435

Sweeney B. W.Funk D. H.Vannote R. L.1986Population genetic structure of two mayflies (Ephemerella subvaria, Eurylophella verisimilis) in the Delaware River drainage basin.Journal of the North American Benthological Society5253262

Thoms M. C.Sheldon F.2000aLowland rivers: an Australian perspective.Regulated Rivers: Research and Management16375383doi:10.1002/1099-1646(200009/10)16:5<375::AID-RRR591>3.0.CO;2-#

Thoms M. C.Sheldon F.2000bWater resource development and hydrological change in a large dryland river: the Barwon–Darling River, Australia.Journal of Hydrology (Amsterdam)2281021doi:10.1016/S0022-1694(99)00191-2

Tockner K.Stanford J. A.2002Riverine flood plains: present state and future trends.Environmental Conservation29308330doi:10.1017/S037689290200022X

Tockner K.Schiemer F.Baumgartner C.Kum G.Weigand al.1999The Danube restoration project: species diversity patterns across connectivity gradients in the floodplain system.Regulated Rivers: Research and Management15245258doi:10.1002/(SICI)1099-1646(199901/06)15:1/3<245::AID-RRR540>3.0.CO;2-G

Tockner K.Malard F.Ward J. V.2000An extension of the flood pulse concept.Hydrological Processes1428612883doi:10.1002/1099-1085(200011/12)14:16/17<2861::AID-HYP124>3.0.CO;2-F

Tooth S.2000Process, form and change in dryland rivers: a review of recent research.Earth-Science Reviews5167107doi:10.1016/S0012-8252(00)00014-3

Torgersen C. E.Price D. M.Li H. W.McIntosh B. A.1999Multiscale thermal refugia and stream habitat associations of chinook salmon in northeastern Oregon.Ecological Applications9301319doi:10.1890/1051-0761(1999)009[0301:MTRASH]2.0.CO;2

Vannote R. L.Minshall G. W.Cummins K. W.Sedell J. R.Cushing C. E.1980The river continuum concept.Canadian Journal of Fisheries and Aquatic Sciences37130137doi:10.1139/F80-017

Walker K. F.Sheldon F.Puckridge J. T.1995An ecological perspective on large dryland rivers.Regulated Rivers: Research and Management1185104doi:10.1002/RRR.3450110108

Waples R. S.1987A multispecies approach to the analysis of gene flow in marine shore fishes.Evolution41385400doi:10.2307/2409146

Ward J. V.Stanford J. A.1995The serial discontinuity concept: extending the model to floodplain rivers.Regulated Rivers: Research and Management10159168doi:10.1002/RRR.3450100211

Ward J. V.Tockner K.Schiemer F.1999Biodiversity of floodplain river ecosystems: ecotones and connectivity.Regulated Rivers: Research and Management15125139doi:10.1002/(SICI)1099-1646(199901/06)15:1/3<125::AID-RRR523>3.0.CO;2-E

Winterbottom J. H.Orton S. E.Hildrew A. G.Lancaster J.1997Field experiments on flow refugia in streams.Freshwater Biology37569580doi:10.1046/J.1365-2427.1997.00184.X

Wood P. J.Petts G. E.1999The influence of drought on chalk stream macroinvertebrates.Hydrological Processes13387399doi:10.1002/(SICI)1099-1085(19990228)13:3<387::AID-HYP745>3.0.CO;2-R

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