Skip to main content

The Cockburn Sound Integrated Ecosystem Model

References


Allan, R.J., & Haylock, M.R. (1993). Circulation features associated with the winter rainfall decrease in southwestern Australia. Journal of Climate, 6(7), 1356–1367. *

Arhonditsis, G.B., & Brett, M.T. (2004). Evaluation of the current state of mechanistic aquatic biogeochemical modeling. Marine Ecology Progress Series, 271, 13–26. *

Baird, M.E., Adams, M.P., Babcock, R.C., Oubelkheir, K., Mongin, M., Wild-Allen, K.A., Skerratt, J., Robson, B.J., Ekau, W., Herzfeld, M., Franklin, C.E., & Margvelashvili, N. (2016). A biophysical representation of seagrass growth for application in a complex shallow-water biogeochemical model. Ecological Modelling, 325, 13–27. *

Bekele, E., Donn, M., Davis, G., Rayner, J., & Furness, A. (2023). Review of surface water drains and likely mass fluxes to Cockburn Sound. Prepared for the WAMSI Westport Marine Science Program. CSIRO, Perth, Western Australia.

BMT (2014). Sepia Depression Ocean Outlet Monitoring and Management Plan. Report 821_001/1_Rev5, prepared for Water Corporation by BMT Oceanica Pty Ltd, Perth, Western Australia. Available HERE

BMT (2018a). Cockburn Sound - Drivers, Pressures, State, Impacts, Responses Assessment 2017: Full Report. Prepared for Department of Water and Environmental Regulation, the Kwinana Industries Council, the City of Rockingham and the City of Kwinana on behalf of the Cockburn Sound Management Council by BMT (Western Australia) Pty Ltd, Report No. 1362_001/1, Perth, Western Australia.

BMT (2018b). Perth Desalination Plant Discharge Modelling: Model Validation. Report prepared for Water Corporation by BMT Eastern Australia, Brisbane, Australia. Available HERE

BMT (2019). Perth Desalination Plant Discharge Modelling: Effects of Desalination Discharges on Dissolved Oxygen. Report R-1334_10-1, prepared for Water Corporation by BMT, Perth, Western Australia. Available HERE

BMTWBM (2023). TUFLOW FV User Manual. BMT Commercial Australia Pty Ltd. Available at https://docs.tuflow.com/TUFLOW-FV/

Boudreau, B.P. (1996). A method-of-lines code for carbon and nutrient diagenesis in aquatic sediments. Computers & Geosciences, 22(5), 479–496.

Boyer, T.P., Baranova, O.K., Coleman, C., Garcia, H.E., Grodsky, A., Locarnini, R.A., Mishonov, A.V., Paver, C.R., Reagan, J.R., Seidov, D., Smolyar, I.V., Weathers, K., & Zweng, M.M. (2018). World Ocean Database 2018. NOAA Atlas NESDIS 87, Silver Spring, MD.

Bruce, L.C., Cook, P.L.M., & Hipsey, M.R. (2015). A model of oxygen and nitrogen biogeochemical response to hydrodynamic regimes in the Yarra River estuary. In: Proceedings of the 21st International Congress on Modelling and Simulation (MODSIM2015). https://doi.org/10.36334/MODSIM.2015.B7.Bruce

Cambridge, M.L., & Hocking, P.J. (1997). Annual primary production and nutrient dynamics of the seagrasses Posidonia sinuosa and Posidonia australis in south-western Australia. Aquatic Botany, 59(3–4), 277–295. *

Cambridge, M.L., & McComb, A.J. (1984). The loss of seagrasses in Cockburn Sound, Western Australia. I. The time course and magnitude of seagrasses decline in relation to industrial development. Aquatic Botany, 20, 229–243.

Cambridge, M.L., Chiffings, A.W., Brittan, C., Moore, L., & McComb, A.J. (1986). The loss of seagrass in Cockburn Sound, Western Australia. II. Possible causes of seagrass decline. Aquatic Botany, 24, 269–285.

Caputi, N., Jackson, G. and Pearce, A. (2014). The marine heat wave off Western Australia during the summer of 2010/11 – 2 years on. Fisheries Research Report No. 250. Department of Fisheries, Western Australia.

Canfield, D.E., Jorgensen, B.B., Fossing, H., Glud, R., Gundersen, J., Ramsing, N.B., Thamdrup, B., Hansen, J.W., Nielsen, L.P., & Hall, P.O.J. (1993). Pathways of organic carbon oxidation in three continental margin sediments. Marine Geology, 113(1–2), 27–40. *

Cary, J.L., Simpson, C.J., & Chase, S. (1995). Water quality in Cockburn Sound: Results of the 1989–1994 Cockburn Sound water quality monitoring programme. Department of Environmental Protection, Technical Series No. 64, Perth, Western Australia. *

Chen, M., Pattiaratchi, C.B., Ghadouani, A., & Hanson, C. (2020). Influence of storm events on chlorophyll distribution along the oligotrophic continental shelf off south-western Australia. Frontiers in Marine Science, 7, 287.

Cockburn Sound Management Council (2009). State of Cockburn Sound 2009 Report. Cockburn Sound Management Council, Perth, Western Australia. *

Collier, C.J., Lavery, P.S., Masini, R., & Ralph, P.J. (2007). Morphological, growth and meadow characteristics of the seagrass Posidonia sinuosa along a depth-related gradient of light availability. Marine Ecology Progress Series, 337, 103–115.

Collier, C.J., Lavery, P.S., Ralph, P.J., & Masini, R.J. (2009). Shade-induced response and recovery of the seagrass Posidonia sinuosa. Journal of Experimental Marine Biology and Ecology, 370(1–2), 89–103. *

D’Adamo, N. (1992). Hydrodynamics and flushing of Cockburn Sound. PhD Thesis, University of Western Australia, Perth, Western Australia. *

D’Adamo, N. (2002). Exchange and mixing in Cockburn Sound, Western Australia: a seasonally stratified, micro-tidal, semi-enclosed coastal embayment. PhD Thesis, Department of Civil Engineering, University of Canterbury, Christchurch, New Zealand. 482 pp.

Dalseno, T.C., Greenwood, J., Keesing, J.K., & Feng, M. (2024). Seasonal deoxygenation in a shallow coastal embayment: The role of stratification and implications for water-quality monitoring. Regional Studies in Marine Science, 77, 103738.

Depinto, J.V., McCulloch, R., Redder, T., Wolfe, J., & Dekker, T. (2010). Deposition and resuspension of particles and the associated chemical transport across the sediment-water interface. In: Sediment and Contaminant Transport in Surface Waters (pp. 253–299). CRC Press. *

Donn, M., Bekele, E., Tapsuwan, S., & McFarlane, D. (2015). Chapter 10 – Managed Aquifer Recharge Scenarios. In: Recycled water for heavy industry and preventing sea water intrusion. McFarlane D.J. (ed.) A report to the Australian Water Recycling Centre of Excellence, Government and industry partners from the CSIRO Land and Water Flagship.

Donn, M., Bekele, E., Wu, H., Prommer, H., Furness, A., Woodbury, R., Rayner, J., & Davis, G. (2025). Baseline assessment of groundwater/surface water nitrogen flux into Cockburn Sound – Final Report. WAMSI Westport Marine Science Program, Project 3.3.4b.

Erftemeijer, P.L.A. (2013). Seagrass Habitat Model – Adelaide’s Coastal Waters. Technical Report WV04758, Sinclair Knight Merz (SKM), Prepared for Deltares and SA Water. https://publications.deltares.nl/1207457.pdf

Erftemeijer, P.L.A., van Gils, J., Fernandes, M.B., Daly, R., van der Heijden, L., & Herman, P.M.J. (2023). Habitat suitability modelling to improve understanding of seagrass loss and recovery and to guide decisions in relation to coastal discharge. Marine Pollution Bulletin, 186, 114370. https://doi.org/10.1016/j.marpolbul.2022.114370

Escudero, C., et al. (2026). [Reference details to be confirmed].

Evans, R.D. (1994). Empirical evidence of the importance of sediment resuspension in lakes. Hydrobiologia, 284(1), 5–12. *

Eyre, B.D., & Ferguson, A.J.P. (2009). Denitrification efficiency for defining critical loads of carbon in shallow coastal ecosystems. Hydrobiologia, 629(1), 137–146. *

Eyre, B.D., van Haastregt, B., Eyre, T.M., & Yeo, S.K. (2025). Cockburn Sound benthic biogeochemistry final report. Prepared for the WAMSI Westport Marine Science Program. Western Australian Marine Science Institution, Perth, Western Australia.

Fofonoff, N.P., & Millard, R.C. Jr. (1983). Algorithms for computation of fundamental properties of seawater. UNESCO Technical Papers in Marine Science, No. 44. UNESCO, Paris. 53 pp. *

Fraser, M.W., & Kendrick, G.A. (2017). Belowground stressors and long-term seagrass decline in a historically degraded seagrass ecosystem after improved water quality. Scientific Reports, 7, 14469. *

Fraser, M.W., Kendrick, G.A., Grierson, P.F., Fourqurean, J.W., Vanderklift, M.A., & Walker, D.I. (2023). Sulfide intrusion in a habitat-forming seagrass can be predicted from relative wave exposure. Frontiers in Marine Science, 10, 1218898. *

Fukumori, I., Wang, O., Fenty, I., Forget, G., Heimbach, P., & Ponte, R.M. (2018). ECCO Version 4 Release 3. Available at: https://ecco.jpl.nasa.gov *

Gallegos, C.L. (2001). Calculating optical water quality targets to restore and protect submersed aquatic vegetation: Overcoming problems in partitioning the diffuse attenuation coefficient for photosynthetically active radiation. Estuaries, 24(3), 381–397. *

Gallegos, C.L., & Moore, K.A. (2000). Factors contributing to water-column light attenuation: A case study from the York River estuary (Chesapeake Bay). Estuaries, 23(2), 231–245. *

Gallop, S.L., Verspecht, F., & Pattiaratchi, C.B. (2012). Sea breezes drive currents on the inner continental shelf off southwest Western Australia. Ocean Dynamics, 62(4), 569–583. *

Ganju, N.K., Defne, Z., Kirwan, M.L., Fagherazzi, S., D’Alpaos, A., & Carniello, L. (2017). Spatially integrative metrics reveal hidden vulnerability of microtidal salt marshes. Nature Communications, 8, 14156. https://doi.org/10.1038/ncomms14156

Gaughan, D.J., & Fletcher, W.J. (1997). Effects of the Leeuwin Current on the distribution of carnivorous macrozooplankton in the shelf waters of south-western Australia. Estuarine, Coastal and Shelf Science, 45(1), 89–97. *

Greenwood, J. (2016). Nitrogen budget for Cockburn Sound, Western Australia. Perth, Western Australia: Report to the Cockburn Sound Management Council and the Western Australian Department of Water, CSIRO.

Greenwood, J., Keesing, J.K., Donn, M.J., & McFarlane, D.J. (2016). Nitrogen Budget for Cockburn Sound, Western Australia. Report to the Cockburn Sound Management Council and the Western Australian Department of Water. CSIRO, Australia.

Gregg, W.W., & Carder, K.L. (1990). A simple spectral solar irradiance model for cloudless maritime atmospheres. Limnology and Oceanography, 35(8), 1657–1675. https://www.numericaloptics.com/doc/HTN4_AtmosphericModel.pdf

Gregg, W.W., & Casey, N.W. (2009). Skill assessment of a spectral ocean-atmosphere radiative model. Journal of Marine Systems, 76, 49–63. https://doi.org/10.1016/j.jmarsys.2008.05.007

Gunaratne, G.L., Suara, K., Lofthouse, E., & Bruce, L. (2023). Development of a water quality response model for Cockburn Sound: An Integrated TUFLOWFV Model. Report A11348, prepared for The University of Western Australia by BMT, 7 March 2023.

Hamilton, D.P., & Schladow, S.G. (1997). Prediction of water quality in lakes and reservoirs. Part I – Model description. Ecological Modelling, 96(1–3), 91–110. *

Hansen, J.E., & Cuttler, M.V.W. (2025). Coastal processes in Cockburn Sound and Owen Anchorage: quantifying baselines and predicting Westport impacts. Prepared for the WAMSI Westport Marine Science Program. Western Australian Marine Science Institution, Perth, Western Australia. 85 pp.

Hobday, A.J. et al. (2016). A hierarchical approach to defining marine heatwaves. Progress in Oceanography, 141, 227–238.

Hobday, A.J. et al. (2018). Categorizing and naming marine heatwaves. Oceanography, 31(2), 162–173.

Hennig, K., Kilminster, K., Kelsey, P., Marillier, B., Hall, J., Gunaratne, G., & Robb, M. (2023). Modelling of the Peel-Harvey Catchment. In F. Valesini, M.R. Hipsey, S. Cronin-O’Reilly, & P. Huang (Eds.), Balancing Estuarine and Societal Health in a Changing Environment. Australian Research Council Project LP150100451. https://aquaticecodynamics.github.io/peel-book/

Hipsey, M.R., Bruce, L.C., & Hamilton, D.P. (2013). Aquatic Ecodynamics (AED) Model Library: Science Manual. The University of Western Australia Technical Manual, Perth, Australia.

Hipsey, M.R., Gal, G., Arhonditsis, G.B., Carey, C.C., Elliott, J.A., Frassl, M.A., Janse, J.H., de Mora, L., & Robson, B.J. (2020). A system of metrics for the assessment and improvement of aquatic ecosystem models. Environmental Modelling & Software, 128, 104697. *

Hipsey, M.R., Busch, B.D., Huang, P., & Boon, C. (2022). AED2: Aquatic Ecodynamics modelling library – Science Manual. The University of Western Australia, Perth, Australia. *

Hipsey, M.R., Huang, P., Zhai, S., Paraska, D., Busch, B., Golder, R., Escuardo, S.G., Fearns, P., & Davies, J. (2025). The Cockburn Sound Integrated Ecosystem Model (CSIEM). Prepared for the WAMSI Westport Marine Science Program. The University of Western Australia, Perth, Western Australia. *

Hovey, R.K., Markey, K., Lyons, M., & Kilminster, K. (2025). Benthic habitat distribution in Cockburn Sound and surrounds. Prepared for the WAMSI Westport Marine Science Program. Western Australian Marine Science Institution, Perth, Western Australia. 72 pp. Available HERE

Hovey, R., & Fraser, M. (2018). Benthic Habitat Mapping of Cockburn Sound. Prepared for: Department of Water and Environmental Regulation and Fremantle Ports, Western Australia.

Huang, P., Hipsey, M., Winter, G., Hetzel, Y., & Hansen, J. (2019). Coastal processes, extreme events and forecasting. In E. J. Techera, & G. Winter (Eds.), Marine Extremes: Ocean Safety, Marine Health and The Blue Economy (pp. 31-47). CRC Press.

Huang, P., Hipsey, M.R., Busch, B., & Hennig, K. (2023). Integrated modelling assessment of nutrient cycling and water quality in the Peel-Harvey Estuary. In F. Valesini, M.R. Hipsey, S. Cronin-O’Reilly, & P. Huang (Eds.), Balancing Estuarine and Societal Health in a Changing Environment. Australian Research Council Project LP150100451. https://aquaticecodynamics.github.io/peel-book/

James, N.P., Collins, L.B., Bone, Y., & Hallock, P. (1999). Subtropical carbonates in a temperate realm: Modern sediments on the southwest Australian shelf. Journal of Sedimentary Research, 69(6), 1297–1321. *

Johnson, D.R., Boyer, T.P., Garcia, H.E., Locarnini, R.A., Baranova, O.K., & Zweng, M.M. (2015). Regional Climatology of the East Asian Seas: An Introduction. NOAA Atlas NESDIS 79, Silver Spring, MD, 37 pp. *

Jørgensen, B.B., Wenzhöfer, F., Egger, M., & Glud, R.N. (2022). Sediment oxygen consumption: Role in the global marine carbon cycle. Earth-Science Reviews, 228, 103987.

Keesing, J.K. (ed.) (2011). Southwest Coastal Ecosystem Characterisation, Benthic Ecology, Connectivity and Client Delivery Modules I. Overview Report. WAMSI Final Report. Western Australian Marine Science Institution, Perth, Western Australia. 23 pp.

Kendrick, G.A., Aylward, M.J., Hegge, B.J., Cambridge, M.L., Hillman, K., Wyllie, A., & Lord, D.A. (2002). Changes in seagrass coverage in Cockburn Sound, Western Australia between 1967 and 1999. Aquatic Botany, 73, 75–87.

Keulen, M. van (1998). Water quality and seagrass biomass, epiphyte and nutrient dynamics in Cockburn Sound, Western Australia. MSc Thesis, Murdoch University, Perth, Western Australia. *

Kim, H.-S., Gangopadhyay, A., Rosenfeld, L.K., & Bub, F.L. (2007). Developing a high-resolution climatology for the Central California coastal region. Continental Shelf Research, 27(16), 2135–2161. https://doi.org/10.1016/j.csr.2007.05.011

Kirkman, H. (1997). Seagrasses of Australia. Prepared for the Department of the Environment, Canberra.

Kirkman, H., & Kirkman, J. (2000). Long-term seagrass meadow monitoring near Perth, Western Australia. Aquatic Botany, 67, 319–332.

Koch, M.S., Benz, R.E., & Rudnick, D.T. (2001). Solid-phase phosphorus pools in highly organic carbonate sediments of northeastern Florida Bay. Estuarine, Coastal and Shelf Science, 52(2), 279–291.

Koslow, J.A., Pesant, S., Feng, M., Pearce, A., Fearns, P., Moore, T., Matear, R., & Waite, A. (2008). The effect of the Leeuwin Current on phytoplankton biomass and production off Southwestern Australia. Journal of Geophysical Research: Oceans, 113(C7), C07050. *

Krause-Jensen, D., Middelboe, A.L., Sand-Jensen, K., & Christensen, P.B. (2000). Eelgrass, Zostera marina, growth along depth gradients: upper boundaries of the variation as a powerful predictive tool. Oikos, 91(2), 233–244. *

Lemmens, J.W.T.J., Clapin, G., Lavery, P., & Cary, J. (1996). Filtering capacity of seagrass meadows and other habitats of Cockburn Sound, Western Australia. Marine Ecology Progress Series, 143, 187–200. *

Levitus, S. (1982). Climatological Atlas of the World Ocean. NOAA Professional Paper 13, US Department of Commerce, National Oceanic and Atmospheric Administration, Rockville, MD, 173 pp. *

Lord, D.A. (2001). The State of Cockburn Sound: A Pressure-State-Response Report. DA Lord & Associates.

Loveless, A., & Oldham, C. (2010). Natural attenuation of nitrogen in groundwater discharging through a sandy beach. Biogeochemistry, 98, 75–87. https://doi.org/10.1007/S10533-009-9377-X

Loveless, A., Oldham, C., & Hancock, G. (2008). Radium isotopes reveal seasonal groundwater inputs to Cockburn Sound, a marine embayment in Western Australia. Journal of Hydrology, 351, 203–217. https://doi.org/10.1016/J.JHYDROL.2007.12.010

Lozano, C.J., Robinson, A.R., Arango, H.G., Gangopadhyay, A., Sloan, N.Q., Haley, P.J., & Leslie, W.G. (1996). An interdisciplinary ocean prediction system: Assimilation strategies and structured data models. In: Malanotte-Rizzoli, P. (Ed.), Modern Approaches to Data Assimilation in Ocean Modeling, Elsevier Oceanography Series, 61, 413–452. *

Mackin, J.E., & Aller, R.C. (1984). Ammonium adsorption in marine sediments. Limnology and Oceanography, 29(2), 250–257.

Masini, R.J., Cary, J.L., Simpson, C.J., & McComb, A.J. (1995). Effects of light and temperature on the photosynthesis of temperate meadow-forming seagrasses in Western Australia. Aquatic Botany, 49(4), 239–254. *

Masselink, G., & Pattiaratchi, C.B. (2001). Characteristics of the sea breeze system in Perth, Western Australia, and its effect on the nearshore wave climate. Journal of Coastal Research, 173–187.

McMahon, K., & Lavery, P.S. (1999). Recovery and resilience of Posidonia australis following anthropogenic disturbance in estuarine waters. Botanica Marina, 42(4), 295–306.

McMahon, K., Lavery, P.S., & Mulligan, M. (1997). Recovery of Posidonia sinuosa seagrass meadows after a major disturbance event: ecological processes and constraints. In: Hancock, D.A. et al. (Eds.), Developing and Sustaining World Fisheries Resources: the State of Science and Management. CSIRO Publishing, Australia.

Middelburg, J.J. (2019). Carbon processing at the seafloor. Springer, 57–75.

Mills, D.A., & D’Adamo, N. (1995). The application of a three-dimensional baroclinic model to the hydrodynamics and transport of coastal waters between Fremantle and Mandurah: The effect of the Garden Island Causeway. Department of Environmental Protection, Technical Series 76, Perth, Western Australia. *

Mitchell, P.J., Yeoh, D.E., Krispyn, K.N., Greenwell, C.N., Cronin-O’Reilly, S., Chabanne, D.B., Hyndes, G.A., Johnston, D., Fairclough, D.V., Wellington, C., & Cottingham, A. (2025). Ecological resources of a heavily modified and utilised temperate coastal embayment: Cockburn Sound. Frontiers in Marine Science, 12, 1563654.

Mohring, M. and Rule, M. (2013). Long-term trends in the condition of seagrass meadows in Cockburn and Warnbro Sounds. Technical Report to the Cockburn Sound Management Council. Department of Parks and Wildlife.

Moore, K.A. (2004). Influence of seagrasses on water quality in shallow regions of the lower Chesapeake Bay. Journal of Coastal Research, Special Issue 45, 162–178. *

Oliver, E.C.J. et al. (2018). Longer and more frequent marine heatwaves over the past century. Nature Communications, 9, 1324.

Paraska, D.W., Hipsey, M.R., & Salmon, S.U. (2021). Sediment diagenesis models: Review of approaches, challenges and opportunities. Environmental Modelling & Software, 145, 105169. *

Paraska, D.W., Zhai, S., Busch, B., Oldham, C.E., Huang, P., Dang, V.H., & Hipsey, M.R. (2021). Hydrological and nutrient modelling of the Swan Canning catchment-estuary system. CRC for Water Sensitive Cities, The University of Western Australia, Perth, Australia.

Pearce, A., Lenanton, R., Jackson, G., Moore, J., Feng, M. and Gaughan, D. (2011). The “marine heat wave” off Western Australia during the summer of 2010/11. Fisheries Research Report No. 222. Department of Fisheries, Western Australia.

Pearce, A.F. and Feng, M. (2013). The rise and fall of the “marine heat wave” off Western Australia during the summer of 2010/2011. Journal of Marine Systems, 111–112, 139–156.

Pearce, A., & Pattiaratchi, C.B. (1999). The Capes Current: a summer countercurrent flowing past Cape Leeuwin and Cape Naturaliste, Western Australia. Continental Shelf Research, 19(3), 401-420.

Pattiaratchi, C., Janekovic, I., & Mahjabin, T. (2024). Provision of multi-decadal ocean boundary conditions and field measurements. Prepared for the WAMSI Westport Marine Science Program. Western Australian Marine Science Institution, Perth, Western Australia. 42 pp. Available HERE

Pattiaratchi, C. (2025). Assessment of infragravity waves. Prepared for the WAMSI Westport Marine Science Program. Western Australian Marine Science Institution, Perth, Western Australia. 42 pp.

Petrone, K.C., Richards, J.S., & Grierson, P.F. (2009). Bioavailability and composition of dissolved organic carbon and nitrogen in a near coastal catchment of south-western Australia. Biogeochemistry, 92(1-2), 27-40. https://doi.org/10.1007/s10533-008-9238-z

Ralph, P.J., Durako, M.J., Enriquez, S., Collier, C.J., & Doblin, M.A. (2007). Impact of light limitation on seagrasses. Journal of Experimental Marine Biology and Ecology, 350(1–2), 176–193. *

Recfishwest (2025). WA’s marine heatwave demands action to build fisheries’ resilience. Published 28 January 2025.

Roberts, K.L., Eate, V.M., Eyre, B.D., Holland, D.P., & Cook, P.L.M. (2012). Hypoxic events stimulate nitrogen recycling in a shallow salt-wedge estuary: The Yarra River Estuary, Australia. Limnology and Oceanography, 57(5), 1427–1442. *

Rose, T.H., Smale, D.A. and Botting, G. (2012). The 2011 marine heat wave in Cockburn Sound, southwest Australia. Ocean Science, 8, 545–550.

Ruiz-Montoya, L., & Lowe, R.J. (2014). Summer circulation dynamics within the Perth coastal waters of southwestern Australia. Continental Shelf Research, 77, 81–95.

Said, N., Webster, C., Dunham, N., Strydom, S., & McMahon, K. (2024a). Current state of knowledge for dredging and climate change impacts on seagrass ecosystems to inform environmental impact assessment and management. A case study: Cockburn Sound and Owen Anchorage. Prepared for the WAMSI Westport Marine Science Program. Western Australian Marine Science Institution, Perth, Western Australia.

Said, N., Webster, C., Dunham, N., Strydom, S., & McMahon, K. (2024b). Seagrass thermal tolerance varies between species and within species across locations. Prepared for the WAMSI Westport Marine Science Program. Western Australian Marine Science Institution, Perth, Western Australia. 26 pp.

Said, N., Webster, C., McMahon, K., Dunham, T., Phelps, C., Frouws, A., Robinson, J., Kilminster, K., & Strydom, S. (2025). Seagrass buried in the dark: reduced light and moderate levels of burial have additive and lethal impacts on Posidonia sinuosa. Prepared for the WAMSI Westport Marine Science Program. Western Australian Marine Science Institution, Perth, Western Australia. 51 pp. HERE

Schlegel, R.W. and Smit, A.J. (2018). heatwaveR: A central algorithm for the detection of heatwaves and cold-spells. Journal of Open Source Software, 3(27), 821.

Seidov, D., Baranova, O.K., Boyer, T.P., Cross, S.L., Mishonov, A.V., & Parsons, A.R. (2018). Northwest Atlantic Regional Climatology. NOAA Atlas NESDIS 80, National Centers for Environmental Information. *

Shahzadi, K., Pinardi, N., Barth, A., Troupin, C., Lyubartsev, V., & Simoncelli, S. (2021). A new global ocean climatology. Frontiers in Environmental Science, 9, 711363. *

Silberstein, R.P., Aryal, S.K., Durrant, J., Pearcey, M., Braccia, M., Charles, S.P., Boniecka, L., Hodgson, G.A., Bari, M.A., Viney, N.R., & McFarlane, D.J. (2012). Climate change and runoff in south-western Australia. Journal of Hydrology, 475, 441–455. *

Skene, D., Ryan, D., Brooke, B., Smith, J., & Radke, L. (2002). The Geomorphology and Sediments of Cockburn Sound. Geoscience Australia Record 2005/10. Geoscience Australia, Canberra. 82 pp.

Skene, D., Ryan, D., Brooke, B., Smith, J., & Radke, L. (2005). The geomorphology and sediments of Cockburn Sound. Geoscience Australia Record 2005/10. Geoscience Australia, Canberra, 82 pp. *

Smale, D.A. and Wernberg, T. (2012). Ecological observations associated with an anomalous warming event at the Houtman Abrolhos Islands, Western Australia. Coral Reefs, 31, 441–441.

Smith, I., & Power, S. (2014). Past and future changes to inflows into Perth (Western Australia) dams. Journal of Hydrology: Regional Studies, 2, 84–96. *

Smith, R.L., Huyer, A., Godfrey, J.S., & Church, J.A. (1991). The Leeuwin Current off Western Australia, 1986–1987. Journal of Physical Oceanography, 21(2), 323–345. *

Steedman, R.K., & Craig, P.D. (1983). Wind-driven circulation of Cockburn Sound. Marine and Freshwater Research, 34(1), 187–212.

Strutton, P.G., Trull, T.W., Phillips, H.E., Duran, E.R., & Pump, S. (2023). Biogeochemical Argo floats reveal the evolution of subsurface chlorophyll and particulate organic carbon in Southeast Indian Ocean eddies. Journal of Geophysical Research: Oceans, 128(4), e2022JC018984. https://doi.org/10.1029/2022JC018984

Strydom, S., Murray, K., Wilson, S., Huntley, B., Rule, M., Heithaus, M., Bessey, C., Kendrick, G.A., Burkholder, D., Fraser, M.W., & Zdunic, K. (2020). Too hot to handle: Unprecedented seagrass death driven by marine heatwave in a World Heritage Area. Global Change Biology, 26(6), 3525–3538. *

Su, C.-H., Eizenberg, N., Steinle, P., Jakob, D., Fox-Hughes, P., White, C.J., Rennie, S., Franklin, C., Dharssi, I., & Zhu, H. (2019). BARRA v1.0: the Bureau of Meteorology Atmospheric high-resolution Regional Reanalysis for Australia. Geoscientific Model Development, 12(5), 2049–2068. *

Tang, C., Li, Y., Acharya, K., Du, W., Gao, X., Luo, L., & Yu, Z. (2019). Impact of intermittent turbulent bursts on sediment resuspension and internal nutrient release in Lake Taihu, China. Environmental Science and Pollution Research, 26(16), 16519–16528. *

Thomson, D.P., Bearham, D., Graham, F. and Eagle, J.V. (2011). High latitude, deeper water coral bleaching at Rottnest Island, Western Australia. Coral Reefs, 30, 1107.

Valesini, F.J., Hipsey, M.R., Eyre, B., Kilminster, K., Plummer, P., Elliott, M., Hallett, C., Huang, P., Busch, B., Wells, N., Hennig, K., Cronin-O’Reilly, S., Reshid, M., Krumholz, O., Horsley, J., & Trinh, J. (2023). Synthesis & Overview. In F. Valesini, M.R. Hipsey, S. Cronin-O’Reilly, & P. Huang (Eds.), Balancing Estuarine and Societal Health in a Changing Environment. Australian Research Council Project LP150100451. https://aquaticecodynamics.github.io/peel-book/

Van Cappellen, P., & Wang, Y. (1995). Metal cycling in surface sediments: modeling the interplay of transport and reaction. Routledge, 21–64.

Van Cappellen, P., & Wang, Y. (1996). Cycling of iron and manganese in surface sediments; a general theory for the coupled transport and reaction of carbon, oxygen, nitrogen, sulfur, iron, and manganese. American Journal of Science, 296(3), 197–243.

van Rijn, L.C. (1993). Principles of Sediment Transport in Rivers, Estuaries, and Coastal Seas. Aqua Publications, Amsterdam, The Netherlands. *

Vieira, V.M.N.C.S., Lopes, I.E., & Creed, J.C. (2018). The biomass–density relationship in seagrasses and its use as an ecological indicator. BMC Ecology, 18, 44. *

Vogwill, R., et al. (2026). [Reference details to be confirmed].

WAMSI (2024). Westport Marine Science Program Theme 2: Seagrass resilience and thermal tolerance. WAMSI Westport Marine Science Program Reports.

Wanninkhof, R. (1992). Relationship between wind speed and gas exchange over the ocean. Journal of Geophysical Research: Oceans, 97(C5), 7373–7382. *

Webster, C., et al. (2024). [Reference details to be confirmed].

Wells, N.S., et al. (2023). The what, where, when and why of nutrient transport to the Peel-Harvey Estuary. In F. Valesini, M.R. Hipsey, S. Cronin-O’Reilly, & P. Huang (Eds.), Balancing Estuarine and Societal Health in a Changing Environment. Australian Research Council Project LP150100451. https://aquaticecodynamics.github.io/peel-book/

Wernberg, T. (2020). Marine heatwave drives collapse of kelp forests in Western Australia. In: Canadell, J.G. and Jackson, R.B. (eds) Ecosystem Collapse and Climate Change. Ecological Studies, Springer-Nature.

Wernberg, T., Smale, D.A., Tuya, F., Thomsen, M.S., Langlois, T.J., de Bettignies, T., Bennett, S. and Rousseaux, C.S. (2012). An extreme climatic event alters marine ecosystem structure in a global biodiversity hotspot. Nature Climate Change, 3, 78–82.

Wijsman, J.W.M., Herman, P.M.J., Middelburg, J.J., & Soetaert, K. (2002). A model for early diagenetic processes in sediments of the continental shelf of the Black Sea. Estuarine, Coastal and Shelf Science, 54(3), 403–421.

Wilson, C., & Wienczugow, K. (2024). Baseline sediment quality survey of Cockburn Sound and Owen Anchorage. Prepared for the WAMSI Westport Marine Science Program. Western Australian Marine Science Institution, Perth, Western Australia. 106 pp.

Wilson, C., & Wienczugow, K. (2025a). Water quality and sediment deposition – December 2022 to December 2023. Prepared for the WAMSI Westport Marine Science Program. Western Australian Marine Science Institution, Perth, Western Australia. 35 pp.

Wilson, C., & Wienczugow, K. (2025b). Water quality of Cockburn Sound and Owen Anchorage – September 2022 to August 2024. Prepared for the WAMSI Westport Marine Science Program. Western Australian Marine Science Institution, Perth, Western Australia. 54 pp.

Winter, G., et al. (2019). [Reference details to be confirmed].

Wunsch, C. (2018). Towards determining uncertainties in global oceanic mean values of heat, salt, and surface elevation. Tellus A: Dynamic Meteorology and Oceanography, 70(1), 1–14. *

Xia, M., et al. (2004). [Reference details to be confirmed].

Xiao, R., Gao, G., Feng, M., Greenwood, J., Keesing, J., Yin, B., … & Lv, X. (2022). Three-dimensional numerical simulation of circulation and vertical temperature structure during summer in Cockburn Sound. Regional Studies in Marine Science, 51, 102187.

Yuan, L.L., & Pollard, A.I. (2018). Changes in the relationship between zooplankton and phytoplankton biomasses across a eutrophication gradient. Limnology and Oceanography, 63(6), 2493–2507.

Zhai, S.Y., Waycott, M., Lewis, R., O’Loughlin, E., Erftemeijer, P.L.A., Huang, P., Brookes, J.D., Sims, C., Zhang, Z., & Hipsey, M.R. (2025). A life stage resolved habitat model for guiding seagrass restoration in coastal lagoons. Ecological Indicators, 170, 113095. https://doi.org/10.1016/j.ecolind.2025.113095

Zhou, C., Liu, D., Keesing, J., Zhao, N., Serrano, O., Masqué, P., Yuan, Z., Jia, Y., & Wang, Y. (2024). Microalgal assemblages response to water quality remediation in coastal waters of Perth, Australia. Marine Pollution Bulletin, 351, 124017.