The Centre for Sustainable Aquatic Ecosystems

People live, work and play near the water. It is a universal challenge to support the many human uses of aquatic ecosystems while also maintaining ecosystem health and biodiversity.

The Centre for Sustainable Aquatic Ecosystems works to ensure healthy and productive freshwater, estuarine and marine ecosystems that continue to support communities across Australia and the Indo-Pacific. We take an integrative socio-ecological approach, with our research focused on sustainable resource use, social and economic benefits and ecosystem health and biodiversity.

Uniquely situated on the rim of the Indian Ocean, the Centre is built on our expertise in aquatic biology and ecology, marine mammal ecology, fisheries, aquaculture, algal biotechnology, oceanography, human-use and habitat assessments, bioinformatics, economics and spatial sciences. Our investigations span all levels of biological organisation from the genome to the ecosystem, and aquatic systems from inland lakes to beyond the continental shelf.

Our core research areas

Fish in hand

Fish biology

Using our historical strengths in the biology and ecology of targeted species for natural fisheries management (from dhufish and whiting to marron and crabs), our focus is on food security through sustainably increasing fish production. This ranges from evaluating restocking programs and the effectiveness of release strategies for fish and invertebrate species, to disease management, closing data gaps in marine stewardship certification of fisheries, and the economics of fisheries.

We also study alternative strategies and opportunities for new fisheries, from evaluating the performance of different types of artificial reefs to assessing aquaculture-based enhancements. Longer-term considerations include climate change adaptation, and we are building our biological monitoring database to model and predict fisheries outcomes under different climate scenarios.


Threatened and flagship species

Understanding the biology, ecology and behaviour of flagship species (such as dolphins, manta rays, whale sharks and various freshwater species) is critical to support biodiversity conservation efforts. This research is extending to creating population distribution models under different climate and human disturbance scenarios, to better manage species–industry interactions including tourism, fisheries, and oil and gas development.

Combinations of new monitoring technologies, in particular tracking devices, drones, and automated image analysis, are allowing us to undertake large-scale surveys of sparsely distributed species such as dugongs and produce results in near-real time.


Catchment-coastal ecosystems and societies

We monitor and model a range of ecological, social and economic health indices and stressors to assess ecosystem health and human impact. Building on these models, we develop predictive decision support systems to explore scenarios and trade-offs in optimising both coastal ecosystem health and human activities. These can inform marine park planning, human-use assessments, and habitat repair and diversification efforts.

Our measurements and models are informed by a number of citizen science programs.

Ocean waves

Biological oceanography

The Indian Ocean is a connected ecosystem, coupling physical, biogeochemical and ecological processes. We have been quantifying decadal change in the water column since the 1960s, and are extending this work to satellite monitoring for remote sensing of oceans.

From characterising nitrogen sources in the open ocean and their impacts on local biogeochemistry to studying food webs around pivotal species, we are better understanding this ecosystem’s climate change adaptation and long-term health.

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Aquaculture and integrated biosystems

Our research informs intensive aquatic food production and quality. From the details of disease management and fish restocking programs through to supply chain considerations and the economics of fish farming, we support modern aquaculture production systems.

Improving the sustainability of these operations is a major focus, through integrating waste products and algal culture biosystems to produce clean water, energy and food.

Our research projects seek to investigate and find novel solutions to complex socio-ecological challenges in aquatic ecosystems.

Fish habitat restoration and release programs

With fish habitats declining in certain areas, the need for alternative restoration and management strategies is becoming apparent. A common approach, particularly in Japan and South East Asia, is to use aquaculture to breed fish and invertebrates such as prawns, and then release them to supplement wild populations.

This can make economic sense, since the numbers of commercially valuable stocks increases, sometimes by hundreds of millions. However, it can also come with a potential environmental cost, if released populations reduce the genetic diversity and long-term fitness of natural populations.

We are looking at ways to increase fish production whilst minimising environmental risk and evaluating socio-economic dimensions that may affect management. This includes the potential effectiveness of releases for fish and invertebrate species, as well as evaluating the performance of different types of artificial reefs or aquaculture programs to replenish fish stocks without the need for captive breeding and release.

Read more about this project on our news site.

Living in harmony with coastal ecosystems

Coastal ecosystems provide vitally important habitats for marine life, but also attract urban development. How can we ensure that both ecosystem health and socio-economic aspirations are protected in developing coastal zones?

This research is aimed at identifying robust indicators of ecological, social and economic health, and producing biophysical and socio-economic models to explore the effect of different development scenarios on these health indicators.

If we have a clear idea of how development plans will influence both ecosystem health and socio-economic health, then we have a rational basis for decision-making.

From waste to waste-not

Producing clean energy and fresh water are two of the principle “wicked” problems of the 21st Century.

These are not new problems and nature discovered a way of doing this millions of years ago. Anaerobic bacteria can feed on organic waste to produce gases (methane) and nutrient-rich effluent, and the nutrients (nitrogen and phosphorous) can be extracted by algae to produce protein (biomass), with clean water as a by-product.

We are trying to harness bacteria and algae in a “biosystem” that produces clean water from organic wastes and to then harvest what the bacteria and algae produce to generate valuable products, such as fish food (from biomass) and renewable energy (from methane gas). The biosystem products and technologies developed through this project will be used to support aquaculture and village facilities in remote areas.

Key researchers


Associate Professor Alan Lymbery

Alan Lymbery is Director of the Centre for Sustainable Aquatic Ecosystems and leads the Aquaculture and Integrated Biosystems research node of the Centre.

Alan’s research is principally in the field of disease ecology, and addresses both conservation challenges facing native freshwater fishes and infectious disease threats to aquaculture species.

Alan works closely with researchers in the Department of Primary Industries and Regional Development on issues facing the health and productivity of Western Australia’s developing aquaculture industry.


Professor Neil Loneragan

Neil Loneragan leads the Fish Biology research node of the Centre. Neil’s research focuses on population biology and ecology of fish and invertebrates (particularly crustaceans); relationships between aquatic habitats and fisheries production and biodiversity; the trophic ecology of estuaries and marine systems; interactions of fisheries with the environment; methods for fisheries assessments; and stock enhancement of recreational and commercial fisheries.

Understanding the complexities of these interactions is necessary if we are to balance between fish stock enhancement for recreational and commercial purpose, and the conservation of natural freshwater and marine environments. Neil’s work extends through Australia and South East Asia.


Dr Fiona Valesini

Fiona Valesini leads the Catchment-coastal Ecosystems and Societies research node.

Fiona is an estuarine ecologist with a particular interest in fish and benthic invertebrate communities and their relationships with the environment.

Her current research, funded by a major ARC-Linkage grant, focuses on indicators of ecosystem health and links to economic and societal well-being in the Peel-Harvey Estuary.

Contact us
Centre Director
Associate Professor Alan Lymbery