Estuarine Research Unit


The Estuarine Research Unit holds an unrivaled fish and invertebrate database for the estuaries of south-western Australia, which has been built progressively since the late 1970s. This data set, containing faunal community records and detailed biological information for most recreationally or commercially targeted species, provides an extremely rare and invaluable basis for understanding long-term ecological ‘change’ in these estuarine systems.

Expertise within the group cover faunal community ecology (assemblage structure and response to environmental drivers, ecosystem function along resource sharing pathways); biology (growth, reproduction, age, mortality, diet); genetics; restocking; fish behaviour and movement patterns; habitat classification and faunal prediction tools and; biotic indices of ecosystem health. The group has also more recently strengthened research linkages to better connect estuarine ecological health response and ecosystem service provision with key catchment drivers.

The Estuarine Research Unit works closely with State management, community and research agencies and has strong international research connections, including through several Adjunct and Distinguished Professor/Collaborator appointments. These international research linkages have facilitated many core comparisons that highlight the unique environmental and ecological features of the micro-tidal estuaries in south-western Australia compared to many of the large macrotidal estuaries of the northern hemisphere.

This section examines some of the work undertaken by the Estuarine Research Unit in 2013-15. For more information, contact Dr Fiona Valesini (

How healthy are our estuaries?

Indicators based on biotic communities are used to monitor and report the ecological condition or health of estuarine ecosystems worldwide, distilling how well the underlying ecosystem structures, processes and functions are operating. However, Australia has been less quick to develop and adopt these core indicators.

With initial funding support from the Swan River Trust, Department of Water, Department of Fisheries and Murdoch University, researchers in the Estuarine Research Group were the first in Australia to develop one such tool, based on fish communities, in 2009/10. This Fish Community Index (FCI) and supporting fish monitoring program has now been used in each year since 2011 to assess and report the condition of the iconic Swan-Canning Estuary, through funding support from the Swan River Trust. This index is also currently being adapted to other estuaries in south-western Australia, including the Walpole-Nornalup.

The FCI combines information on a suite of ‘metrics’, each of which quantifies an aspect of the structure and/or function of estuarine fish communities and responds to a range of stressors affecting the ecosystem (Fig. 1). These metrics are measured from the fish monitoring data, then compared to historical ‘reference conditions’ that represent the
best ecosystem condition observed over the last 30-40 years. Establishing these references has been made possible through the extensive fish community data sets collected by the CFFR in the Swan-Canning Estuary since the late 1970s. Metrics are scored based on their deviation from these benchmarks, then integrated into a final FCI score (0‒100) and a corresponding ‘report card’ grade (A; very good ‒ E; very poor) that reflects the overall condition of the estuary and its various zones (Fig. 2).

Radar plot

Fig. 1: Example of the metrics used to calculate the Fish Community Index (No species, number of species; Sh-Wiener, Shannon-Wiener diversity; No trop spec, number of trophic specialists; No trop gen, number of trophic generalists; Prop detr, proportion of detrivores; Prop benthic, proportion of benthic species; Prop est spawn, proportion of estuarine spawning species).

Offshore FCI 2015 Swan Canning

Fig. 2: Example of the FCI ‘report card’ grades in the offshore waters of each major zone of the Swan-Canning Estuary in summer and autumn 2015.

Prawning in the Swan River

At the end of a long, hot summer Perth day, it was typical to see lanterns and fires around the Swan and Canning rivers, where generations of West Aussies would go to catch and cook a bucket of prawns. Western School Prawn (Metapenaeus dalli) numbers declined steadily throught the 1990s, to the point where only a handful of ardent recreational prawners were left by 2000. Community concern about this issue led to a collaboration between the Australian Centre for Applied Aquaculture Research (ACAAR), the Swan River Trust (SRT) and the CFFR (funded by the Recreational Fishing Initiatives Fund, Fisheries Research Development Corporation and SRT) to launch a restocking program for this species. This program, which began in 2013 and continues through 2016, has three main aims; (1) produce juvenile prawns via aquaculture for restocking into the estuary (led by Greg Jenkins, ACAAR); (2) undertake biological and ecological studies of this prawn species to maximise restocking success (led by James Tweedley and Neil Loneragan, CFFR); and (3) engage and educate the community through developing a dedicated citizen science program (led by Kerry Trayler, SRT).

Aquaculturists at ACAAR achieved a world first by culturing eggs from gravid (pregnant) females collected from the estuary and growing them through the naupliar, protozoeal, mysis and initial post-larval stages to produce juvenile prawns for release. The far smaller size of Western School Prawns compared to other cultured prawns initially proved challenging, with only ~1,000 prawns being bred and released in summer 2013. The development of novel aquaculture methods by the ACAAR team to overcome these difficulties has since led to the release of ~630,000 prawns in 2014 and~2 million in 2015.


Successful growth of many species in aquaculture is typically supported by extensive data on their biology and ecology. However, this was not the case with M. dalli, where little such information existed. To fill this knowledge gap, research effort in the current project was focused in three areas, namely larval growth and development, biology and ecology, and maximising restocking success. The larval work is being undertaken by PhD student Jason Crisp. Jason’s research has firstly described larval development and has since determined the optimum temperature and salinity for survival and growth. He is now working on determining the most effective microalgal feeds and a protocol for identifying broodstock in peak reproductive condition. Ecological studies of the prawns (i.e. their spatial and temporal distribution in the estuary and potential environmental drivers) are being led by PhD student Brian Poh and Dr James Tweedley, who have undertaken an extensive sampling program in the shallow and deeper waters of the system in every month for two and a half years. Brian is currently correlating patterns in prawn abundance with a range of environmental variables. Brian is also investigating the genetic implications of restocking the Western School Prawn in the Swan River Estuary. Honours student Amber Bennett (who submitted her thesis in 2014) also examined the sediment preference of this prawn species through complementary field sampling and laboratory experiments. Andrew Broadley, who also completed his Honours project in 2014, determined a range of biological characteristics of M. dalli including timing of reproduction, size/weight at reproduction and growth and mortality rates. Andrew is now undertaking a PhD in the CFFR, and is using the above characteristics to determine prawn biomass in the system and develop a bio-economic model to determine the costs and benefits of restocking.

Work is also being undertaken by Brian and current student Kyle Hodgson to identify the fish species that predate on juvenile prawns.

Community engagement
A citizen science program for recreational prawners, ‘Prawn Watch’, was established by SRT in 2013 with the aim of (1) re-engaging people with prawning in the Swan-Canning Estuary; (2) educating the community on the prawn species in the system and sustainable fishing practices; (3) collecting data on the spatial and temporal abundances of prawn species targeted by recreational fishers; and (4) aiding collection of prawn broodstock for the aquaculture component of the project. Multiple community training events have been held across the metropolitan area. Waterproof logbooks and a Smartphone application were also developed and provided to all participants to aid collection of robust data by recreational prawners.

More details about Prawn Watch can be found at:
For information about prawning go to:

A quarter of a century of Black Bream research

The Black Bream (Acanthopagrus butcheri) is arguably the most important recreational fish species in the estuaries of southern Australia and also contributes to the commercial fishery in some of these systems. This species is thus of enormous social and economic value. During the last 25 years, Ian Potter and numerous excellent research students and postdoctoral fellows, including Gavin Sarre, Margaret Platell and Ben Chuwen, have studied various aspects of the biology of this iconic species in several key estuaries on the lower west and south coasts of Western Australia.

Biological characteristics of Black Bream

Recently, the Recreational Fishing Initiatives Fund (RFIF) us to collect data on Black Bream in nine key estuaries across south-western Australia, which could then be incorporated into the massive dataset collected by the CFFR since the early to mid-1990s for this species. The aim of this study is to compare the biological characteristics of Black Bream in different estuarine environments and over time to produce a composite picture of these characteristics. The results will enable recreational and commercial fishers to understand fully how the biological characteristics of this highly adaptable species vary among estuaries and alter in response to environmental changes. They will also provide fisheries and environmental managers with key data for conserving this important species. Joel Williams (Post-doctoral research fellow), whose PhD was on the biology of Black Bream in the Gippsland Lakes in Victoria, and PhD students Alan Cottingham and Eloise Ashworth are playing a crucial role in this RFIF project. Recreational and commercial fishers are being very helpful with tagging studies and in providing frames of Black Bream. Joel is responsible for running the complex field sampling program and tagging studies and is using his expertise to explore, through sampling larval Black Bream, some of the factors that influence recruitment, such as the volume of freshwater flow.

Tagging fish at the Grand Final National Bream fishing competition

Alan Cottingham’s study has demonstrated that, in the Swan River Estuary between the early 1990s and mid-2000s, the growth, body condition and length at maturity of Black Bream has declined and age at maturity has increased (Fig. 1). These changes parallel declines in rainfall and thus reduced flushing of the estuary, thereby leading to a decline in oxygen concentrations in the deeper waters of the system. Fish densities in these deeper areas have declined while those in the nearshore shallow waters have increased, suggesting an onshore migration of this species to avoid the reduced environmental quality of the offshore waters. The greater densities of fish in the shallows accounts, at least in part, for the above changes in the biological characteristics of Black Bream. This study was funded by the Swan River Trust, Department of Fisheries, Department of Water and Murdoch University.  Eloise Ashworth’s PhD involves developing a new model, derived from otolith measurements, to produce more reliable back-calculated estimates of the lengths of fish at different ages. This will allow determination of the extent to which fish growth is influenced by inter-annual variation in environmental factors, such as temperature. Her project employs data from previous CFFR studies on not only Black Bream, but also Mulloway, Foxfish, Breaksea Cod, Estuary Cod and Dhufish. The form of generalised growth model that best described the relationships between fish lengths and age at capture, and between otolith radius and age at capture, was determined for each species. The lengths and otolith radii, predicted by the somatic and otolith growth curves for fish of different ages, were then used to describe the relationship between expected fish length and expected otolith radius for fish of the same age. A back-calculation approach, which employed this relationship and thus allowed for the changes in somatic and otolith growth rates throughout the life of fish, was then developed and tested. The study is developing well and will highlight differences in the pattern of growth among species and the relationship of growth to environmental variables.

Swan growth curves.jpg

Fig. 1: Changes in the growth of female (top) and male (bottom) Black Bream in the Swan-Canning Estuary from the mid-1990’s to late 2000s

Restocking the Blackwood River Estuary

A marked decline in the numbers of Black Bream in the Blackwood River Estuary led to a project, funded by the Fisheries Research and Development Corporation, Western Australian Fishing Foundation and Recfishwest, which was aimed at determining whether restocking was an effective way of replenishing depleted populations of this species. Greg Jenkins and his colleagues at the Australian Restocking the Blackwood River Estuary. A marked decline in the numbers of Black Bream in the Blackwood River Estuary led to a project, funded by the Fisheries Research and Development Corporation, Western Australian Fishing Foundation and Recfishwest, which was aimed at determining whether restocking was an effective way of replenishing depleted populations of this species. Greg Jenkins and his colleagues at the Australian Centre for Applied Aquaculture Research, thus cultured juvenile Black Bream and stained their otoliths (ear bones) with Alizarin complexone, after which they were released into the Blackwood River Estuary in 2002 and 2003. As the pink stain in the middle of the otoliths still remains visible, the progress of these restocked Black Bream has been able to be followed for 13 years. The results show that restocked fish perform nearly as well as wild stock and can make a major contribution to the recreational and commercial fisheries and also contribute to future generations. A study of the genetic implications of this restocking program was also recently completed.


Energetics and movement dynamics of Black Bream

Nathan Beerkens Honours project involves performing lab experiments on Black Bream across a range of temperatures and dissolved oxygen concentrations to determine how well they are able to function at each level.  Ultimately, this will help us to understand how the fish may cope with environmental changes to the Swan-Canning estuary, such as warming temperatures and the low-oxygen conditions created by algal blooms. Nathan’s project is kindly assisted by Challenger TAFE, Fremantle, funded by Recfishwest and Murdoch University and supervised by Dr Adrian Gleiss and Dr Stephen Beatty.

Respirometry Experiments (7).JPG

Fish tracking and ecology in the Walpole and Nornalup Inlets Marine Park

The Estuarine Research Unit is re-visiting the Walpole-Nornalup Inlet system, one of the only permanently-open estuaries on the south coast of Western Australia and one of just three gazetted Marine Parks in estuaries State-wide, to re-examine its fish communities for the first time in over 20 years and track the movement patterns of key species targeted by recreational fishers.

In a collaborative project funded by the WA Department of Fisheries and Murdoch University, PhD student Daniel Yeoh will assess (1) spatial and temporal differences in the fish faunas throughout the estuary, including how they may have changed since the early 90s; (2) movement patterns of Black Bream, Southern Bluespotted Flathead, Pink Snapper and Tarwhine using acoustic telemetry; and (3) the ability to develop a fish-based index of estuarine health to track the ongoing ecological condition of this Marine Park. Supported by additional funding from Recfishwest, Dan is also developing community engagement activities to promote greater understanding of sustainable fishing practices and estuarine health. The Walpole-Nornalup is a popular eco-tourism and recreational fishing destination, and this project has generated considerable interest and support among the fishing community.

Seasonal sampling of fish assemblages throughout the Walpole-Nornalup began in July 2014, and has so far yielded 43 species from 27 families. Preliminary data analyses indicate marked differences in fish species composition between regions of the estuary, seasons and between day and night. An array of 17 acoustic receivers has also been deployed throughout the estuary to track individual fish tagged internally with acoustic transmitters. With the assistance of local recreational fishers, 23 Black Bream and 16 Southern Bluespotted Flathead have so far been tagged.

Swan Fish Track

The oxygenation plants in the Swan River, Perth, are designed to enhance the water quality and health of the system during periods of low oxygen. However, how fish respond to the plants has not been determined. This new project will acoustically track Black Bream using the Department of Parks and Wildlife’s new Swan Canning Acoustic Array to determine how their movements and habitat use relate to the water quality conditions in the Swan River, and how those movements specifically respond to operation of the oxygenation plants.

Information gathered will be of direct use by managers in understanding fish response to the oxygenation plants. Recfishwest have provided funding for the acoustic tags and the recreational fishing community have been instrumental in helping to catch larger fish to tag. Two Honours students (Jake Watsham and Nathan Beerkens) are working on the project with Jake focussing on the acoustic data, and Nathan undertaking complementary studies on the physiology of black bream in the laboratory. Project leads are Stephen Beatty and Adrian Gleiss.


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