Step 4: Flow Ecology Linkages

Step 4: Flow Ecology Linkages

What does the model discuss?

The relationships between altered flow and ecological characteristics and empirical testing of these relationships with existing and new field data is a cornerstone of the ELOHA approach. Similarly, the hypothesis that the form of these relationships is consistent within major river types is another key element; hence the importance of river classification (see Step 2 -River classification).

Formulating flow alteration – ecological response relationships

Poff et al. (2010[1]) suggest that river ecologists possess a good general knowledge of the importance of flow to riverine ecology but that specific responses to specific changes in hydrology is less well known. Empirical models that directly predict ecological responses to various types of hydrologic variation are not readily available. As a result it is necessary to develop hypotheses about such response and to test them using available data to determine their veracity. Poff et al. (2010[1]) provide a list of example hypotheses (their Table 1) and some examples are included here in Table 4.1

Warfe et al. (2011[2])( reviews our knowledge of the importance of the flow regime in influencing ecology of northern Australian rivers. It is a very useful summary of our knowledge of flow ecology relationships in the region and can be validly used to generate hypotheses about flow ecology relationships. From this and other research, TRaCK has compiled a list of guidelines for water management agencies that was developed from the collective experience of TRaCK researchers (see Step 4 – Related resources and projects). The guidelines are, in some cases, essentially hypotheses about flow ecology responses (albeit with empirical support).  Others, especially those relating to monitoring and social aspects of water management, are the result of experience or direct empirical examination of prior hypotheses (i.e. they have been tested by experience or the acquisition of data).

Other guidelines will be highlighted where they apply to monitoring, planning, social values and implementation within the Social Process component of the ELOHA framework.

Compiling ecological data to test-flow ecology relationships

Ecological responses to flow alteration are diverse and may occur through direct or indirect means. Direct responses involve organismal dependencies on the flow regime such as reliance on flow related cues for reproduction or migration. Indirect responses are usually mediated by changes in habitat or water quality that, in turn, impact on a diverse array of features such as habitat suitability, productivity, connectivity and migration pathways, predation and competition dynamics, and physiological tolerances.

Table 4.1: Examples of hypotheses to describe ecological responses to flow alteration (from Poff etal. 2010)

Extreme low flow

Hyp: Depletion of extreme low flows in perennial stream and subsequent drying will lead to a a rapid loss of biodiversity and biomass in invertebrates and fish due to declines in wetted riffle habitat, lowered residual pool area/depth when riffles stop flowing, loss of connectivity between viable habitat patches and poor water quality.

Low flow

Depeletion of low flows will lead to progressive reduction in total secondary production as habitat area becomes marginal in quality or is lost

Small floods/high flow pulses

Increased frequency of substrate-disturbing events leads to a shift toward ‘weedy’ invertebrate species and loss of species with poor colonising abilities

Large floods

Lessened frequency or extent of floodplain inundation will lead to reduced invertebrate and fish production or biomass due to loss of flooded habitat and food resources supporting growth and recruitment



  1. Poff, N.L., et al. The ecological limits of hydrologic alteration (ELOHA): a new framework for developing regional environmental flow standards. Freshwater Biology 55, 147-170 (2010).
  2. Warfe, D.M., et al. The “wet-dry” in the wet-dry tropics drives river ecosystem structure and processes in northern Australia. Freshwater Biology 56, 2169-2195 (2011).


Related projects & resources


The importance of river flows to the ecology of the region's aquatic biota and the processes that sustain biodiversity has been a key theme of TRaCK’s research. The outcomes of that research provides a rich source of information upon which hypotheses about flow ecology relationships can be formulated and tested.

Warfe et al. (2011[1]) ( summarises our understanding of the relationship between ecology and water regime in rivers of the wet-dry tropics of northern Australia.

The various relevant TRaCK research projects are highlighted below as are links to fact sheets, reports and other communication material associated with these projects. The user should also consult the TRaCK Digital Atlas to determine the availability of data sets that have arisen from these projects.

5.1 Bottom up and top down control of tropical river floodplains

The food webs of Australia's tropical rivers are poorly understood yet provide the foundation for healthy rivers.  This project explores how these food webs are structured to support complex river ecosystems.  Using a variety of experiments scientists identify the sources of organic matter which kick-start tropical river food webs, which animals exert a strong control in the food chain, how land and water based food webs relate to one another and how these factors relate to water regime.

5.2: Refugial Pools. Importance of waterholes as aquatic refugia and the biophysical processes that sustain them

River waterholes are a critical refuge for aquatic plants and animals when rivers stop flowing and are also highly valued by local communities.  Unfortunately waterholes are also vulnerable to increasing water demands, uncontrolled stock access, fishing pressure and the effects of climate change.  This study examined how waterholes in northern Australia respond to such pressures.

5.3 River floodplain food web susbsidies

As the wet season flows overtop river banks, fish and other animals make the most of expanded feeding grounds, moving out onto the floodplains.  As the floodwaters recede, these animals take the nutrients and energy obtained from the floodplain, back to the river channel.  This project examined floodplain food webs, quantifying the contribution of subsidies to, and from the floodplain, and determined how some current land management practices are affecting the floodplain food webs of northern rivers.

5.4: Assessing the effect of urbanisation and catchment development on ecosystem health in estuaries

This project assessed the effects of different land-based development pressures on the assets and values of northern estuarine ecosystems.  Research focussed initially on the effects of urban development in Darwin Harbour.  The second part of the project focus on the effects of agriculture and potential water resource development in the southern estuaries of the Gulf of Carpentaria, in particular, the potential impacts on young prawns.

5.5: Flow-ecology relationships for biodiversity and ecosystem processes

Water managed and 'allocated' to the environment is commonly known as 'environmental flows'.  The critical step in determining appropriate environmental flows is predicting how particular changes in river flows might affect natural ecological assets[2].  This project investigated the relationships between flow and several specific assets of tropical rivers.

5.6: Flow impacts on estuarine finfish of the Gulf of Carpentaria

Our current knowledge suggests that flows of freshwater into estuaries play a significant role in determining the numbers of fish that live there.  This project examined how freshwater flows affect some key estuarine species.  This knowledge is crucial if we are to manage water resources in a manner that minimizes negative impacts on estuaries.

5.7: Environmental flow tools for northern rivers

There is growing interest in developing and allocating the water resources of tropical Australia.  The big question is how much water can we extract for water development and how much do we need to retain to sustainably manage the ecological health of aquatic systems?  This project derive a set of guidelines for people managing tropical rivers that help them decide on how to allocate water to the environment.

5.8: Biodiversity and HCVAE: Bioregionalisation conservation priorities and predictivemodels of aquatic biodiversity

Biodiversity is a feature of aquatic ecosystems that is often valued by different members of the community.  To effectively manage aquatic biodiversity, we need to know where the areas of high biodiversity are.  It is also useful to know what causes some areas to have high biodiversity and others not.  This project provides the answers to these questions and defines biologically unique regions (bioregions) within northern Australia based on patterns of aquatic biodiversity.

The report detailing an examination of the distribution of high conservation value assets (also known as high value ecological assets) can be found at

This report details the distribution of different habitat types and biotic groups (fish, bugs, turtles and waterbirds) across the region, how different diversity and conservation value attributes can be combined to define conservation value and identifies areas of high conservation value. It also details the application of a systematic conservation planning approach to assess the optimal size and configuration of protected areas needed to protect northern Australia’s unique aquatic biodiversity.

A fact sheet about the project can be accessed at

The various GIS layers used in that assessment can be accessed on the TRaCK Digital Atlas.

5.9 Northern Australia Aquatic Ecological Assets

The Northern Australia Water Futures Assessment (NAWFA) is an Australian Government initiative to provide the science needed for sustainable development and protection of Northern Australia’s water resources. One project being undertaken as part of the NAWFA Ecological Program is the TRaCK Northern Australia Ecological Assets Project.

4.4: Bedload transport in large tropical rivers and its effect on dry-season pool habitat dynamics

The pools that remain in northern Australian rivers during the long dry season provide an important refuge for stream fauna and flora and are often culturally significant. There is a common perception, however, that many of these riverine waterholes are being filled by sands. Changes in land-use upstream and the effects of climate change have been suggested as causes for sand accumulation. This project will determine, whether there is evidence for sustained infilling of pools within two north Australian river catchments.

4.6: Trial of the Framework for the Assessment of River and Wetland Health (FARWH) in the wet/dry tropics

The National Water Commission has developed a national framework that can form the basis of comparable national river and wetland health assessments, and has the capacity to bring together results of existing broad-scale assessments conducted at state, territory and basin scales. The Framework for the Assessment of River and Wetland Health (FARWH) was trialled by TRaCK to evaluate the effectiveness of the Framework to assess river health in the wet/dry tropics, and contribute to north Australian river management. Access to the report can be gained at:

Flow management guidelines

A series of guidelines relating to environmental water management and assessment was produced based on the outcomes of the research project listed above. The guidelines can be accessed at [Water Guidelines].

Distribution of aquatic organisms – the spatial arrangement of biodiversity

As part of TRaCk’s research on the natural resources of northern Australian freshwaters, a series of data sets documenting the distribution of different elements of aquatic biodiversity have been compiled. Some of these data sets (e.g. waterbirds and turtles) were obtained from other researchers and are not therefore widely available. They are available upon request however in some circumstances and information on contact details is available from the metadata database associated with the TRaCK Digital atlas (

Freshwater Fish Atlas

The TRaCK digital Freshwater Fish Atlas builds on the Northern Australia Freshwater Fish (NAFF) Atlas hosted at The TRaCK Freshwater Fish Atlas differs from the NAFF atlas in some key aspects. First, the data set upon which it is based (6698 locations with either single or multispecies data) has been aggregated to 2328 subcatchments (planning units). Thus, species lists are available for planning units but not individual locations (i.e. sampling points). Aggregation of locations up to the scale of subcatchments has been achieved through the use of predictive modeling, thus the maps available as part of the Freshwater fish Atlas also show the distribution of species in parts of the landscape which have not been surveyed but for which the model predicts a species to occur.

The TRaCK Freshwater Fish Atlas allows information of fish biodiversity to be accessed in several ways. First, species lists for individual catchments can be downloaded. Second, the distribution of 105 species can be accessed either as maps individually plotted (on the map function associated with the Digital Atlas) or as GIS shape files.

Other spatial information associated with the distribution of freshwater fish such as species richness, endemicity, phylogenetic distinctiveness etc. can be accessed via the Digital Atlas. Similar spatial information is available for bugs, turtles and waterbirds at this location.

Bibliography: Distribution of Freshwater Fishes

A bibliography of literature dealing with the distribution of freshwater fishes (bibliography fish distributions.pdf) can be accessed at

Reports detailing the fish fauna and management needs of the Norman River ( and of Cape York Peninsula ( provide useful information on flow ecology relationships in these areas.

A bibliography (northern aquatic biodiversity bibliography.pdf) of literature dealing with the aquatic biodiversity of northern Australia can be accessed at [provide link]. It contains references relevant to aquatic plants and riparian vegetation, aquatic macroinvertebrates, fish, frogs, turtles, aquatic snakes and lizards, and birds. It also contains references to threats, impacts and management needs.

Research Centres

There are a number of Australian research centres focussed on northern Australian freshwaters and the biota they support. They provide a rich source of information upon which hypotheses about flow ecology relationships can be formed and tested.

The Australian Centre for Tropical Freshwater Research (ACTFR) at James Cook University is one such Centre ( Access to reports concerning the management of freshwater habitats and biota can be found at

Issues covered include, for example,

Environmental Research Institute of the Supervising Scientist (ERISS)

ERISS is primarily tasked with monitoring and investigating the impacts associated with uranium mining in the Kakadu region. Its scientists are also active in many other areas of research related to aquatic biodiversity and management and reports associated with these activities can be accessed at ERISS researchers were involved in a large collaborative project entitled the Tropical River Inventory and Asssessment Projectwhich is a rich resource of information concerning the aquatic biodiversity of northern Australia.The reports associated with this project A Compendium of Ecological Information on Australia's Northern Tropical Rivers - Sub project 1 of Australia's Tropical Rivers - an integrated data assessment and analysis (DET18) and Ecological risk assessments for Australia's Northern Tropical Rivers - Sub project 2 of Australia's Tropical Rivers - an integrated data assessment and analysis (DET18) are especially useful and can be accessed at and

State Government Agencies

The various state government agencies associated with managing the water resources of northern Australia also hold significant information on the biota and biology of the region.These holdings for the Northern Territory can be accessed at; for Western Australia, at; and for Queensland, at

Federal Agencies

The National Water Commission (NWC) is responsible for driving progress towards the sustainable management and use of Australia's water resources under our blueprint for water reform - the National Water Initiative. Reports commission by the NWC are primarily concerned with the policy of water management but are also relevant to the management of water resources to sustain biodiversity. The can be accessed at

The Department of Sustainability, Environment, Water, Population and Communities ( is responsible for implementing the Australian Government's policies to protect our environment and heritage, and to promote a sustainable way of life. Information on biodiversity can be accessed at and reports and other publications may be accessed at


  1. Warfe, D.M., et al. The “wet-dry” in the wet-dry tropics drives river ecosystem structure and processes in northern Australia. Freshwater Biology 56, 2169-2195 (2011).
  2. Chan, T.U., et al. Bayesian network models for environmental flow decision making in the Daly River, Northern Territory, Australia. River Research and Applications (In Press).at <>


Environmental water terminology

A top down environmental water assessment method used in Queensland in which ecological condition is assessed against known deviations from the natural or pre-development flow regime whilst also taking into account the impacts of water infrastructure on ecological condition.
Bottom–up methods
Reconstructing an altered flow regime by sequentially adding water needed for specific functions i.e. adding a flushing flow designed to move refine sediment or a maintenance flow designed to provide a minimum amount of wetted area.
Cultural flows
Water required to meet the cultural and spiritual needs of Indigenous people. Environmental flows A term that supplanted the term instream flows in recognition that water was needed for more than just the maintenance of habitat quality and quality. Water is needed to provide cues for biota to move and to reproduce, to provide areas for food production, for refuge from temperature extremes, for maintenance of channel form and substrate composition, to create and maintain new habitats such as floodplains and tributaries, and many other needs.
Environmental water
A term that supplants the term environmental flows in recognition that flowing water is not the only water critical to the maintenance of ecosystem function. Hyporheic water (water held under the stream bed) and groundwater are also critical compartments of environmental water and groundwater dependent aquatic habitats may never be connected to the riverine environment.
Holistic flow management
A conceptual framework first described in 1992 in which water needs are considered more broadly than just those relating to in-stream or in-channel needs e.g. estuaries and the near shore marine environment are dependent on freshwater inputs as are riparian forests and off-channel wetlands.
Hyporheic water
(water held under the stream bed) and groundwater are also critical compartments of environmental water and groundwater dependent aquatic habitats may never be connected to the riverine environment.
Instream flow incremental methodology: a computer driven means of assessing changes in in-channel habitat quantity and quality.
Instream flows
The original term for environmental flow management, principally concerned with the maintenance of habitat quantity and quality defined by depth, water velocity and substrate composition. Typically, instream flow investigations of were undertaken at small spatial scales – i.e. at the reach scale.
Top-down methods
Environmental water assessment methods in which occurs the simulated sequential removal of volumes of water until an impact of nominated severity occurs, thus defining the limit below which this aspect of the flow regime can be altered.

ELOHA process navigator

ELOHA Process navigator Use this navigator to move around the ELOHA process  Hydrologic Foundation River classification River classification Flow Alteration Flow-ecology linkagesSocial processesMonitoring