WAMSI-Westport Marine Science Program

Development of an integrated ecosystem model that will provide an understanding of how water quality and marine habitats may change under various potential future scenarios.  

• Project 1.1: Cockburn Sound Integrated Ecosystem Model Platform
  
  

• Project 1.2: in progress

1.3 Characterising the trophic structure, ecosystem attributes and functioning of Cockburn Sound through conceptual, qualitative and quantitative ecosystem models: This component synthesises existing ecological knowledge to develop conceptual and qualitative models describing key species, trophic pathways and pressures, and uses these to inform a quantitative Ecopath model that establishes a baseline understanding of ecosystem functioning. Together, these models clarify how biological communities, environmental drivers and human activities interact, providing the analytical foundation required to assess cumulative impacts and support ecosystem‑based management of Cockburn Sound.

• Project 1.3: Using conceptual, qualitative and quantitative ecosystem models to characterise the trophic structure, ecosystem attributes and functioning of Cockburn Sound

Enhance knowledge of benthic ecosystem structure and function in Cockburn Sound, with emphasis on the drivers, pressures and processes that influence seagrass condition, resilience, rehabilitation and restoration outcomes.

2.1 Benthic Habitat mapping: This project delivers contemporary, high resolution benthic habitat maps for Cockburn Sound, Owen Anchorage and Gage Roads. It compiles existing datasets, undertakes targeted field surveys, and resolves key spatial knowledge gaps to meet Environmental Impact Assessment (EIA) requirements. The resulting habitat baseline provides essential spatial context for assessing ecological condition, planning future monitoring, and informing management of benthic ecosystems. 

• Project 2.1: Benthic habitat distribution in Cockburn Sound and surrounds

2.2 Pressure-response relationships, building resilience and future proofing seagrass meadows: Understanding how the multiple pressures, including light limitation, sedimentation, warming and historical stressors can influence the tolerance thresholds and long-term resilience of temperate seagrasses. It examines the drivers of ongoing seagrass decline in Cockburn Sound and evaluates mechanisms to reverse degradation, strengthen resilience and future-proof meadows against dredging and climate-related impacts. Outcomes support EIA processes by defining thresholds, indicators and management actions for protecting vulnerable seagrass species.

• Project 2.2: Current state of knowledge for dredging and climate change impacts on seagrass ecosystems to inform environmental impact assessment and management

• Project 2.2: Resilience of seagrass Posidonia sinuosa is negatively affected by high levels of burial of dredged material 

• Project 2.2: Seagrass thermal tolerance varies between species and within species across locations

• Project 2.2: Two decades of seagrass monitoring data show drivers include ENSO, climate warming and local stressors

• Project 2.2: Posidonia sinuosa tolerates the cumulative effects of a short-term heatwave and low light event

• Project 2.2: Thermal priming of dehisced Posidonia seed does not increase thermal tolerance in establishing seedlings

• Project 2.2: Seagrass buried in the dark: reduced light and moderate levels of burial have additive and lethal impacts on Posidonia sinuos

• Project 2.2: Population genomics of Posidonia sinuosa

• Project 2.2 Executive Summary: Key findings to inform Environmental Impact Assessment and Management for the proposed Westport development and for managing and building resilience under a changing climate in temperate seagrass communities

• Project 2.2: Drivers of seagrass decline in Perth waters and actions to halt decline

• Project 2.2 Appendix A: Ephemeral seagrass meadow assessment to improve understanding of resilience of ephemeral seagrasses on Kwinana Shelf for Environmental Impact Assessment and Management

• Project 2.2 Appendix B: Enhanced resilience to prolonged marine heatwaves in seagrass Posidonia sinuosa populations from warmer regions

• Project 2.2 Appendix C: Ongoing recovery measurements in Kwinana Shelf seagrass meadow in Cockburn Sound 2.5 years post impact phase to give greater confidence in recovery data and for EIA monitoring

2.3 Seagrass restoration program: This project will advance seagrass restoration in Cockburn Sound, Kwinana Shelf, and Owen Anchorage, aiming to restore areas commensurate with historical losses. It will implement trials using seed-based and shoot-based methods, informed by best practice and emerging science. Seagrass restoration in Cockburn Sound aims to scale up seed and sprig planting, improve habitat conditions, and use assisted migration to boost resilience against dredging and climate change, supported by mechanisation and community programs like Seeds for Snapper. 

• Project 2.3: Review of past seagrass restoration projects and guidelines for restoration in Cockburn Sound

• Project 2.3: Seagrass Restoration - Final Report

2.4 Benthic communities in soft-sediment and hard substrates (baseline data, pressure-response relationships of key biota for Environmental Impact Assessment), and mitigation strategies for artificial reefs: Investigating the composition of soft sediment and hard substrate communities, the pressure-response relationships of key macroinvertebrate in relation to EIA, and the optimal locations and materials for potential mitigation strategies using artificial reefs to support biodiversity and offset ecological impacts.

• Project 2.4: Benthic communities in soft-sediment and on natural hard habitats

• Project 2.4: Pressure-response relationships of key invertebrates to total suspended solid concentrations and sedimentation

• Project 2.4: Benthic communities on hard substrates: small scale feasibility trials for artificial reefs

• Project 2.4: Investigation of material preference and the role of ‘green walls’ in inhibiting the establishment of invasive marine species on port infrastructure

Develop a comprehensive environmental baseline and understand contaminants, nutrient sources, and recycling.

3.1 Water and sediment quality monitoring: project aims to provide updated baseline data useful for understanding the current state of Cockburn Sound. The project will provide contextual/input data for programs such as water quality modelling, seagrass rehabilitation and any other WAMSI Science programs requiring background water quality information. Existing potential threats to water and sediment quality in Cockburn Sound and the vicinity of the proposed Port will be identified.

• Project 3.1: Baseline Sediment Quality Survey of Cockburn Sound and Owen Anchorage April 2023

• Project 3.1: Water quality toxicant snapshot survey and diffusive gradient thin films September 2023

• Project 3.1: Water Quality and Sediment Deposition – December 2022 to December 2023

• Project 3.1: Water quality of Cockburn Sound and Owen Anchorage - September 2022 to August 2024

3.2 was rescoped and elements were included in Project 3.4 and 3.5. 

3.3 Elements of the groundwater/surface water flux into Cockburn Sound: The project aims to understand the connection between shallow and deep discharging aquifers and controls on seawater intrusion to define the aquitard layer between two key shallow aquifers. It will identify saltwater intrusion and the thickness of the saltwater wedge at either or both aquifers. Pre-existing and new data will be integrated, and a model-based interpretation of data for the estimation of groundwater and nutrient fluxes.

• Project 3.3: Review of surface water drains and likely mass fluxes to Cockburn Sound

• Project 3.3: Flow, transport and biogeochemical reaction mechanisms affecting nitrogen discharge from groundwater into Cockburn Sound, Western Australia

• Project 3.3: Baseline assessment of groundwater/surface water nitrogen flux into Cockburn Sound - Final Report

• Project 3.3: Baseline Nutrient Fluxes into Cockburn Sound: Uncertainty Quantification via a History-Matched Groundwater Model with an Ensemble of Parameter Sets

3.4 Sediment sulphides, oxygen flux and seagrass health: This project will determine sulphide intrusion thresholds for Cockburn Sound seagrasses through controlled mesocosm experiments, assessing how sediment properties and light influence vulnerability. Findings will inform management of seagrass health under changing environmental conditions.

• Project 3.4: Unravelling the effects of sediment hydrogen sulfide on Posidonia sinuosa metabolism, microbiome and health

3.5 Cockburn Sound benthic nutrient flux dynamics: Examining the benthic biogeochemical processes in Cockburn Sound to inform Westport’s environmental planning. It quantifies sediment oxygen demand, organic matter decomposition, and nutrient fluxes across 12 major benthic habitats, including seagrass and mud basin sites. The study also evaluates denitrification efficiency and its role in nitrogen removal, highlighting how benthic autotrophy versus heterotrophy influences nutrient cycling.

• Project 3.5: Cockburn Sound benthic biogeochemistry - Final Report

Understand seasonal movements of key species, the habitats they seek out and the food they rely on.

4.1 Snapper connectivity and evaluation of juvenile stocking: Understanding the significance of snapper spawning aggregations in Cockburn Sound in relation to the broader west coast stock, and the longevity of hatchery-reared juvenile snapper in the wild in relation to re-stocking as a potential mitigation strategy.

• Project 4.1: Snapper connectivity and evaluation of juvenile stocking 

4.2.1 Spatial distribution and temporal variability in life stages of key fish species in Cockburn Sound: Investigating the spatial and temporal patterns in the distributions of different life stages of key fishes, the habitat use by key fishes in relation to environmental variables in Cockburn Sound, and recruitment patterns of key fish species.

• Project 4.2: Spatial distribution and temporal variability in life stages of key fish species in Cockburn Sound 

4.2.2 Zooplankton in Cockburn Sound: Looking at the spatial and temporal patterns in the distributions of zooplankton and drivers of change, the distribution of fish larvae in relation to environmental factors, methods to identify and monitor disturbance and change in zooplankton communities.

• Project 4.2 Zooplankton in Cockburn Sound (Ichthyoplankton); description of larval assemblage and dispersal modelling of key fishery species

4.2.3 Trophic pathways and food web structure: Investigating the gut content and stable isotope analyses to describe energy and nutrient flows from primary producers to higher trophic levels in Cockburn Sound and Owen Anchorage. Sampling across seasons and regions will focus on key commercial species and prey for seabirds, informing EIA, climate change assessments, and resilience strategies for ecosystem productivity.

• Project 4.2: Trophic pathways and food web structure of Cockburn Sound and Owen Anchorage 

• Project 4.2: Zooplankton in Cockburn Sound 

4.3 Investigating effects of climate change on biota in Cockburn Sound: This project will assess the direct and indirect impacts of climate change on fish and invertebrates in Cockburn Sound, including habitat shifts and species adaptation to warming conditions. Using statistical models and risk assessments, it will analyse biological-environmental relationships and extreme events, providing a baseline for EIA and future resilience planning.

• Project 4.3: Investigating effects of climate change on biota in Cockburn Sound 

4.4 Effects of total suspended solids on key fish species:  experiments were conducted to assess the impacts of total suspended solids on key fish species including effects on foraging, gill function, habitat selection, and egg survival. Results will provide critical data for evaluating dredging-related risks in Cockburn Sound.

• Project 4.4: The effects of total suspended sediment associated with dredging on fishes: a review and management strategies

4.5 was rescoped and elements were included project 4.7.

4.6 was rescoped and elements were included in project 4.7. 

4.7 Investigating effect of Westport Development on invasive species risks to Cockburn Sound: This project will establish contemporary reference levels of metals and pesticides in key commercial and recreational fish and shellfish species in Cockburn Sound. Using eight representative species across trophic levels, it will provide a baseline for future monitoring and address community concerns about potential contamination from port activities, informed by limited historical data.

• Project 4.7: Marine invasive species literature review

5.1 Hydrodynamic modelling: Developing high-resolution hydrodynamic models for Cockburn Sound using open ocean boundary conditions from UWA’s Regional Ocean Modelling System and future climate scenarios. It includes collecting oceanographic data on currents and light conditions for model validation, providing essential inputs for accurate environmental and impact assessments.

• Project 5.1: Provision of multi-decadal ocean boundary conditions and field measurements 

5.2 Surface gravity wave modelling: There are two parts to this project, one will investigate infragravity waves and their influence on coastal processes in Cockburn Sound. By analysing field measurements and model outputs, it will improve understanding of low-frequency wave energy and its implications for sediment transport and habitat stability. The other part of the project (second project component/etc) will develop hindcast wave models to characterise historical wave conditions in Cockburn Sound and Owen Anchorage. It will provide essential data for validating hydrodynamic models and assessing long-term wave dynamics relevant to port development and environmental planning.

• Project 5.2: Hindcast surface gravity wave modelling 

• Project 5.2: Assessment of infragravity waves

Identify and understand the community values connected to Cockburn Sound.

6.1 Community values for changes in environmental conditions: Identifying environmental qualities and functions of Cockburn Sound valued by the Perth community, including willingness to pay and trade-offs for potential impacts from port development. It provides a baseline measure of social licence and socio-economic values to inform EIA and mitigation strategies, incorporating monetisation of environmental and social externalities through a cost-benefit approach.

• Project 6.1: Community values for environmental assets in Cockburn Sound 

• Project 6.1: Community values for environmental assets in Cockburn Sound - Appendices 

6.2 Opportunities and impacts for recreational fishing from the Westport development: Assessing recreational fishers’ perceptions and the actual impacts of port development on fishing practices using a mixed-methods social science and economics approach. It will identify both risks and opportunities, such as artificial reefs, seagrass restoration, and snapper stocking, providing critical insights for social licence and socio-economic components of the EIA.

• Project 6.2: Opportunities and impacts for recreational fishing from the Westport development Final Report 

6.3 Recreation, amenity and aesthetic values: Assessing the recreational uses of Cockburn Sound beyond fishing, using participatory GIS mapping, literature review, and stakeholder consultation to identify activities, values, and potential conflicts from development. It will apply non-market valuation surveys to quantify recreational demand and willingness to pay, informing EIA on significant effects to amenity and aesthetic values.

• Project 6.3: Spatial mapping of non-fishing recreational activities and associated values in Cockburn Sound, Western Australia

6.4 Benefit-cost framework for environmental port design features: Developing a benefit-cost framework to evaluate port and breakwater design options and mitigation measures, integrating financial, social, and environmental outcomes. The framework aims to maximise environmental and social benefits while supporting informed decision-making for sustainable port development.

• Project 6.4: Evaluating suitability of investing in environmental enhancements in Cockburn Sound: A benefit-cost analysis of port design features

Develop current and future underwater ‘soundscapes’ of Cockburn Sound to understand, and manage, the potential effects of underwater noise.

7.1 Baseline soundscape, sound sources and transmission: Establishing a baseline underwater soundscape for Cockburn Sound, identifying sound sources and transmission patterns. It focuses on understanding risks to sensitive marine fauna, including effects on foraging, navigation, reproduction, and communication

• Project 7.1: Baseline soundscape, sound sources and transmission (Final Report)

7.2 Hearing sensitivity of Australian sea lions, little penguins, and fish: there are three sub projects to this project examining the hearing sensitivity and noise susceptibility of Australian sea lions, little penguins, and snapper.  

• Project 7.2: Hearing in Australian sea lions 

• Project 7.2: Hearing in little penguins 

• Project 7.2: Hearing in Cockburn Sound snapper

7.3 Behavioural response of fish to noise: Determining the hearing sensitivity of fish species in Cockburn Sound and identify noise thresholds that trigger behavioural responses. 

• Project 7.3: Anthropogenic noise effects on a member of the Sparidae family: A literature review with otolith modelling and implications for coastal development 

Improve the understanding of the distribution and seasonal movements of conservation-significant and iconic species, the habitats they seek out and the food sources they rely on.

8.1 Determining the diet, causes of mortality, foraging habitat and home range of little penguins using Cockburn Sound: Investigating the foraging behaviour, diet composition, and causes of mortality of Little Penguins in Cockburn Sound. Using DNA from faecal samples and stable isotope analysis of chick feathers, it will track annual and seasonal diet changes, identify mortality trends, and map foraging habitats and home ranges of breeding penguins.

• Project 8.1: Determining the diet, causes of mortality, foraging habitat and home range of Little Penguins using Cockburn Sound

• Project 8.1: Options to mitigate potential starvation of penguins during the Westport dredging campaign - review and recommendations 

8.2 Investigate the abundance, movement, habitat use and diet of Australian sea lions in the Perth Metropolitan area: This project will map foraging areas and assess habitat use of Australian sea lions in Cockburn Sound, alongside identifying and quantifying key prey species.  

• Project 8.2: Australian sea lion abundance and movement in the Perth metropolitan area, Western Australia - Final Report 

8.3 Spatio-temporal distribution of key habitat-uses and key prey species for Indo-Pacific bottlenose dolphins in Owen Anchorage and Cockburn Sound, including a fine-scale understanding of the use of the habitats in the Kwinana Shelf: collecting baseline data on Indo-Pacific bottlenose dolphins in Cockburn Sound, focusing on foraging and nursing habitats, abundance, and distribution. 

• Project 8.3: Broad-scale distribution and habitat modelling of Indo-Pacific bottlenose dolphins (Tursiops aduncus) in Owen Anchorage and Cockburn Sound using boat-based survey data from 2011-2015 

• Project 8.3: Trophic ecology of Indo-Pacific dolphins (Tursiops aduncus) in Owen Anchorage and Cockburn Sound inferred by stable isotopes 

• Project 8.3: Fine-scale understanding of Indo-Pacific bottlenose dolphin use of the Kwinana Shelf within Cockburn Sound and identification of key areas within the Shelf

8.4 Spatio-temporal distribution of syngnathids in Cockburn Sound: Reviewing the state of knowledge on syngnathid fishes (seahorses, pipefishes, and sea dragons) in Cockburn Sound and Owen Anchorage, providing baseline data on distribution and habitat.

• Project 8.4: Spatio-temporal distribution of syngnathid fishes in Cockburn Sound and Owen Anchorage
  
  

9.1 Coastal processes and sediment movement in Cockburn Sound and Owen Anchorage: This study established baseline coastal processes in Cockburn Sound and Owen Anchorage, revealing that 45% of the shoreline is eroding and that Parmelia and Success Banks are critical sediment sources for beaches.

• Project 9.1: Coastal processes in Cockburn Sound and Owen Anchorage - quantifying baselines and predicting Westport impacts