References
Alilou, H., Oldham, C., McFarlane, D., Hipsey, M.R., 2022. A structured framework to interpret hydro-climatic and water quality trends in Mediterranean climate zones, Journal of Hydrology 614, 128512.
Allen, R.G., Pereira, L.S., Raes, D., Smith, M., 1998. Crop evapotranspiration - Guidelines for computing crop water requirements - FAO Irrigation and drainage paper 56, Food and Agriculture Organization, Rome.
Almroth-Rosell, E., Edman, M., Eilola, K., Markus Meier, H.E., Sahlberg, J., 2016. Modelling nutrient retention in the coastal zone of an eutrophic sea, Biogeosciences 13, 5753–5769. https://doi.org/10.5194/bg-13-5753-2016
Anderson, M.J., Gorley, R.N., Clarke, K.R., 2008. PERMANOVA+ for PRIMER: Guide to software and statistical methods. PRIMER-E Ltd.
ANZECC, 2000. Australian and New Zealand Guidelines for Fresh and Marine Water Quality. Australian; New Zealand Environment; Conservation Council.
Atkins, J.P., Burdon, D., Eliott, M., Gregory, A.J., 2011. Management of the marine environment: integrating ecosystem services and societal benefits with the DPSIR framework in a systems approach, Marine Pollution Bulletin 62(2), 215–226.
Barnard, S., Elliott, M., 2015. The 10-tenets of adaptive management and sustainability: An holistic framework for understanding and managing the socio-ecological system, Environmental Science & Policy 51, 181–191.
Bates, B.C., Hope, P., Ryan, B., Smith, I., Charles, S., 2008. Key findings from the Indian Ocean Climate Initiative and their impact on policy development in Australia, Climate Change 89, 339–354. https://doi.org/10.1007/s10584-007-9390-9
Beesley, P.L., Ross, G.J., Glasby, C.J., 2000. Polychaetes & allies: The southern synthesis. CSIRO Publishing, Melbourne.
Bernhardt, E.S., Blaszczak, J.R., Ficken, C.D., Fork, M.L., Kaiser, K.E., Seybold, E.C., 2017. Control points in ecosystems: moving beyond the hot spot hot moment concept, Ecosystems 20, 665—682.
BMT, 2023a. TUFLOW-FV science manual. BMT, Brisbane.
BMT, 2023b. Https://www.tuflow.com/downloads/tuflow-fv-archive/, 2019.01.008 release (version 2019.01.008) [software]. BMT, Brisbane.
Booth, E.G., Qiu, J., Carpenter, S.R., Schatz, J., Chen, X., Kucharik, C.J., Loheide, S., Motew, M., Seifert, M., J. Turner, 2016. From qualitative to quantitative environmental scenarios: Translating storylines into biophysical modeling inputs at the watershed scale, Environmental Modelling & Software 85, 80–97.
Borja, Á., Franco, J., Pérez, V., 2000. A marine biotic index to establish the ecological quality of soft-bottom benthos within European estuarine and coastal environments, Marine Pollution Bulletin 40, 1100–1114. https://doi.org/10.1016/S0025-326X(00)00061-8
Bradby, K., 1997. Peel-Harvey: the decline and rescue of an ecosystem. Greening the Catchment Taskforce Inc., Mandurah.
Brearley, A., 2005. Ernest Hodgkin’s Swanland: The estuaries and coastal lagoons of south-western australia. UWA Publishing, Perth, WA.
Bruce, L.C., Cook, P.L.M., Teakle, I., Hipsey, M.R., 2014. Hydrodynamic controls on oxygen dynamics in a riverine salt wedge estuary, the yarra river estuary, australia, Hydrology and Earth System Sciences 18, 1397–1411. https://doi.org/10.5194/hess-18-1397-2014
Bryan, B.A., Crossman, N.D., King, D., Meyer, W.S., 2011. Landscape futures analysis: Assessing the impacts of environmental targets under alternative spatial policy options and future scenarios, Environmental Modelling & Software 26(1), 83–91.
Burdige, D.J., 2011. Estuarine and coastal sediments–coupled biogeochemical cycling, Treatise on Estuarine and Coastal Science 5, 279—308.
Bureau of Meteorology, 2017. Special Climate Statement 60—heavy rainfall and flooding in southwest Western Australia. Australian Government, Bureau of Meteorology, Commonwealth of Australia.
Busch, B., Hipsey, M.R., Huang, P., others, 2023. AquaticEcoDynamics/peel_ARC: Data, model & document repository [dataset]. https://doi.org/https://doi.org/10.5281/zenodo.**********
Carpenter, S.R., Booth, E.G., Gillon, S., Kucharik, C.J., Loheide, S., Mase, A.S., Motew, M., Qiu, J., Rissman, R., A., Seifert, J., Soylu, E., Turner, M., Wardropper, C.B., 2015. Plausible futures of a social-ecological system: Yahara watershed, wisconsin, USA, Ecology and Society 20(2), 10.
Chilton, D., Hamilton, D.P., Nagelkerken, I., Cook, P., Hipsey, M.R., Reid, R., Sheaves, M., Waltham, N.J., Brookes, J., 2021. Environmental Flow Requirements of Estuaries: Providing Resilience to Current and Future Climate and Direct Anthropogenic Changes, Frontiers in Environmental Science 9, 764218.
Clarke, K.R., Gorley, R.N., 2015. Getting started with PRIMER v7. PRIMER-E Ltd.
Cloern, J.E., Jassby, A.D., Schraga, T.S., Nejad, E., Martin, C., 2017. Ecosystem variability along the estuarine salinity gradient: Examples from long-term study of san francisco bay, Limnology and Oceanography 62, S272–S291. https://doi.org/10.1002/lno.10537
Conley, D.J., Carstensen, J., Ertebjerg, G., Christensen, P.B., Dalsgaard, T., Hansen, J.L., Josefson, A.B., 2007. Long-term changes and impacts of hypoxia in Danish coastal waters, Ecological Applications 17, S165—S184.
Cormier, R., Elliott, M., Rice, J., 2019. Putting on a bow-tie to sort out who does what and why in the complex arena of marine policy and management, Science of the Total Environment 648, 293–305.
Cottingham, A., Hesp, S.A., Hall, N.G., Hipsey, M.R., Potter, I.C., 2014. Marked deleterious changes in the condition, growth and maturity schedules of Acanthopagrus butcheri (Sparidae) in an estuary reflect environmental degradation, Estuarine, Coastal and Shelf Science 149, 109–119. https://doi.org/10.1016/j.ecss.2014.07.021
Cronin-OReilly, S., Wells, N.S., McCallum, R., Hallett, C.S., Tweedley, J.R., Valesini, F.J., Eyre, B.D., 2022. Chronically stressed benthic macroinvertebrate communities exhibit limited effects on ecosystem function in a microtidal estuary, Marine Ecology Progress Series 701, 1–16.
Dauvin, J.C., Ruellet, T., 2007. Polychaete/amphipod ratio revisited, Marine Pollution Bulletin 55, 215–224. https://doi.org/10.1016/j.marpolbul.2006.08.045
Davies, C.L., Surridge, B.W., Gooddy, D.C., 2014. Phosphate oxygen isotopes within aquatic ecosystems: Global data synthesis and future research priorities, Science of the Total Environment 496, 563—575.
Department of Planning, Lands and Heritage, 2018. Perth and peel at 3.5 million, Western Australian Planning Commission.
Department of Regional Development, 2014. Summary/Structure of the Key Elements of the Regional Blueprint for Integrated Regional Growth and Development, Western Australian.
Diaz, R.J., Rosenberg, R., 1995. Marine benthic hypoxia: A review of its ecological effects and the behavioural responses of benthic macrofauna, Oceanography and Marine Biology: An Annual Review 33, 245–303.
Ducharne, A., Baubion, C., Beaudoin, N., Benoit, M., Billen, G., Brisson, N., others,. Long term prospective of the seine river system: Confronting climatic and direct anthropogenic changes, Science of Total Environment 375, 292–311. https://doi.org/10.1016/j.scitotenv.2006.12.011
Elliott, M., Burdon, D., Atkins, J.P., Borja, A., Cormier, R., De Jonge, V.N., Turner, R.K., 2017. And DPSIR begat DAPSI(W)R(M)!”-a unifying framework for marine environmental management, Marine Pollution Bulletin 118(1-2), 27–40.
Elliott, M., Mander, L., Mazik, K., Simenstad, C., Valesini, F., Whitfield, A., Wolanski, E., 2016. Ecoengineering with Ecohydrology: Successes and failures in estuarine restoration, Estuarine, Coastal and Shelf Science 176, 12–35.
Elshafei, Y., Tonts, M., Sivapalan, M., Hipsey, M.R., 2016. Sensitivity of emergent sociohydrologic dynamics to internal system properties and external sociopolitical factors: Implications for water management, Water Resources Research 52, 4944–4966.
Eyre, B.D., 2000. Regional evaluation of nutrient transformation and phytoplankton growth in nine river-dominated sub-tropical east australian estuaries, Marine Ecology Progress Series 205, 61–83.
Eyre, B.D., Ferguson, A.J., 2009. Denitrification efficiency for defining critical loads of carbon in shallow coastal ecosystems, in: Eutrophication in Coastal Ecosystems. Springer, p. 137—146.
Ferreira, J.G., Wolff, W.J., Simas, T.C., Bricker, S.B., 2005. Does biodiversity of estuarine phytoplankton depend on hydrology?, Ecological Modelling 187, 513–523. https://doi.org/10.1016/j.ecolmodel.2005.03.013
Fofonoff, N.P., Millard, R.C., 1983. Algorithms for computation of fundamental properties of seawater, UNESCO Technical Papers in Marine Sciences 44. https://doi.org/10.25607/OBP-1450
Gabrielson, J.O., 1981. The Sediment Contribution to Nutrient Cycling in the Peel/Harvey Estuarine System: a technical report to Department of Conservation and Environment, EPA Bulletin No. 96. Unpublished Technical Report. Environmental Protection Authority, Perth, Western Australia.
Gamenick, I., Jahn, A., Vopel, K., Giere, O., 1996. Hypoxia and sulphide as structuring factors in a macrozoobenthic community on the Baltic Sea shore: Colonisation studies and tolerance experiments, Marine Ecology Progress Series 144, 73–85. https://doi.org/10.3354/meps144073
Gee, J.H., Gee, P.A., 1991. Reactions of gobioid fishes to hypoxia: buoyancy control and aquatic surface respiration, Copeia 17—28.
Gooddy, D.C., Lapworth, D.J., Bennett, S.A., Heaton, T.H., Williams, P.J., Surridge, B.W., 2016. A multi-stable isotope framework to understand eutrophication in aquatic ecosystems, Water Research 88, 623—633.
Gorley, A.M., Clarke, K., 2008. PERMANOVA+ for PRIMER: guide to software and statistical methods, PRIMER-E: Plymouth, UK.
Graham, L.P., 2004. Climate change effects on river flow to the baltic sea, Ambio 33, 235–241.
Greening, H., Janicki, A., Sherwood, E.T., Pribble, R., Johansson, J.O.R., 2014. Ecosystem responses to long-term nutrient management in an urban estuary: Tampa bay, Estuarine, Coastal and Shelf Science 151, A1–A16.
Hale, S.S., Cicchetti, G., Deacutis, C.F., 2016. Eutrophication and hypoxia diminish ecosystem functions of benthic communities in a New England estuary, Frontiers in Marine Science 3, 249.
Hallett, C.S., 2018. Assessment of the condition of the Swan Canning Estuary in 2018, based on the Fish Community Index of estuarine condition. Unpublished report. Murdoch University, Perth, Western Australia.
Hallett, C.S., 2014. Quantile-based grading improves the effectiveness of a multimetric index as a tool for communicating estuarine condition, Ecological Indicators 39, 84—87.
Hallett, C.S., Hall, N.G., 2012. Equivalence factors for standardizing catch data across multiple beach seine nets to account for differences in relative bias, Estuarine, Coastal and Shelf Science 104, 114—122.
Hallett, C.S., Hobday, A.J., Tweedley, J.R., Thompson, P.A., McMahon, K., Valesini, F.J., 2018. Observed and predicted impacts of climate change on the estuaries of south-western Australia, a Mediterranean climate region, Regional Environmental Change 18, 1357—1373.
Hallett, C.S., Trayler, K.M., Valesini, F.J., 2019a. The Fish Community Index: A Practical Management Tool for Monitoring and Reporting Estuarine Ecological Condition, Integrated Environmental Assessment and Management 15, 726—738.
Hallett, C.S., Valesini, F., Elliott, M., 2016a. A review of Australian approaches for monitoring, assessing and reporting estuarine condition: III. Evaluation against international best practice and recommendations for the future, Environmental Science & Policy 66, 282–291.
Hallett, C.S., Valesini, F.J., Clarke, K.R., 2012a. A method for selecting health index metrics in the absence of independent measures of ecological condition, Ecological Indicators 19, 240—252.
Hallett, C.S., Valesini, F.J., Clarke, K.R., Hesp, S.A., Hoeksema, S.D., 2012b. Development and validation of fish-based, multimetric indices for assessing the ecological health of western australian estuaries, Estuarine, Coastal and Shelf Science 104-105, 102–113.
Hallett, Chris S., Valesini, F.J., Elliott, M., 2016. A review of Australian approaches for monitoring, assessing and reporting estuarine condition: I. International context and evaluation criteria, Environmental Science & Policy 66, 260—269.
Hallett, C.S., Valesini, F.J., Kilminster, K., Wells, N.S., Eyre, B.D., 2019b. A rapid protocol for assessing sediment condition in eutrophic estuaries, Environmental Science: Processes & Impacts 21, 1021–1037. https://doi.org/10.1039/C9EM00141G
Hallett, C.S., Valesini, F., Scanes, P., Crawford, C., Gillanders, B.M., Pope, A., Udy, J., Fortune, J., Townsend, S., Barton, J., Ye, Q., Ross, D.J., Martin, K., Glasby, T., Maxwell, P., 2016b. A review of Australian approaches for monitoring, assessing and reporting estuarine condition: II. State and Territory programs, Environmental Science & Policy 66, 270–281.
Hargrave, B.T., Holmer, M., Newcombe, C.P., 2008. Towards a classification of organic enrichment in marine sediments based on biogeochemical indicators, Marine Pollution Bulletin 56, 810—824.
Heal, K.V., Bartosova, A., Hipsey, M.R., Chen, X., Buytaert, W., Li, H.Y., McGrane, S.J., Gupta, A.B., Cudennec, C., 2022. Ensuring consideration of water quality in nexus approaches in the science–practice continuum: reply to discussion of “Water quality: the missing dimension of water in the water–energy–food nexus?, hydrological Sciences Journal 67, 1291–1293.
Heal, K.V., Bartosova, A., Hipsey, M.R., Chen, X., Buytaert, W., Li, H.Y., McGrane, S.J., Gupta, A.B., Cudennec, C., 2021. Water quality: The missing dimension of water in the water–energy–food nexus, hydrological Sciences Journal 66, 745–758.
Hennessy, K.B., Fitzharris, B.C., Bates, N., Harvey, S.M., Howden, L., Hughes, J., others, 2007. Australia and new zealand. Climate change 2007: Impacts adaptation and vulnerability. Contribution of working group II to the fourth assessment report of the intergovernmental panel on climate change. Cambridge University Press, Cambridge, UK,.
Hennig, K., Kelsey, P., 2015. Avon Basin Hydrological and Nutrient Modelling, Water Science Technical Series, Report No. 74, Department of Water and Environmental Regulation, Western Australia.
Hennig, K., Kelsey, P., Hall, J., Gunaratne, G.G., Robb, M., 2021. Hydrological and nutrient modelling of the peel-harvey catchment. Water science technical series, report no. 84. Department of Water; Environmental Regulation, Western Australia.
Hipsey, M.R., 2022. Modelling aquatic eco-dynamics: Overview of the AED modular simulation platform. Zenodo repository. https://doi.org/10.5281/zenodo.6516222
Hipsey, M.R., G., 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., Hamilton, D.P., Hanson, P.C., Carey, C.C., Coletti, J.Z., Read, J.S., Ibelings, B.W., Valesini, F.J., Brookes, J.D., 2015. Predicting the resilience and recovery of aquatic systems: A framework for model evolution within environmental observatories, Water Resources Research 51(9), 7023–7043.
Hirst, A.J., 2004. Broad-scale environmental gradients among estuarine benthic macrofaunal assemblages of south-eastern Australia: Implications for monitoring estuaries, Marine and Freshwater Research 55, 79–92. https://doi.org/10.1071/MF03011
Hodgkin, E.P., Birch, P.B., Black, R.E., Humphries, R.B., 1980. The Peel-Harvey estuarine system study (1976–1980): A report to the Estuarine & Marine Advisory Committee, December 1980, Department of Conservation and Environment.
Hogberg, P., 1997. Tansley review No.95 15N natural abundance in soil-plant systems, New Phytologist 137, 179—203.
Honti, M., Schuwirth, N., Rieckermann, J., Stamm, C., 2017. Can integrative catchment management mitigate future water quality issues caused by climate change and socio-economic development?, Hydrology and Earth System Sciences 21, 1593–1609.
Howarth, R., Chan, F., Conley, D.J., Garnier, J., Doney, S.C., Marino, R., Billen, G., 2011. Coupled biogeochemical cycles: Eutrophication and hypoxia in temperate estuaries and coastal marine ecosystems, Frontiers in Ecology and the Environment 9, 18–26.
Howarth, R.W., Marino, R., 2006. Nitrogen as the limiting nutrient for eutrophication in coastal marine ecosystems: Evolving views over three decades, Limnology and Oceanography 51, 364–376.
Huang, P., Hennig, K., Kala, J., J., A., Hipsey, M.R., 2000. Climate change overtakes coastal engineering as the dominant driver of hydrological change in a large shallow lagoon, Hydrology and Earth System Sciences 24, 5673–5697. https://doi.org/10.5194/hess-24-5673-2020
Huang, P., Hipsey, M.R., Pritchard, D., 2017. Hydrologic evolution due to an artificial channel and climate change in the Peel-Harvey Estuary, Proceedings of the 37th IAHR World Congress.
Huang, P., Kilminster, K., Larsen, S., Hipsey, M.R., 2018. Assessing artificial oxygenation in a riverine salt-wedge estuary with a three-dimensional finite-volume model, Ecological Engineering 118, 111–125. https://doi.org/10.1016/j.ecoleng.2018.04.020
Huang, P., Trayler, K., Wang, B., Saeed, A., Oldham, C.E., Busch, B., Hipsey, M.R., 2019. An integrated modelling system for water quality forecasting in an urban eutrophic estuary: The swan-canning estuary virtual observatory, Journal of Marine Systems 199, 103218.
Hugues-dit-Ciles, J., Kelsey, P., Marillier, B., Robb, M., Forbes, V., McKenna, M., 2012. Leschenault estuary water quality improvement plan, Department of Water and Environmental Regulation, Western Australia.
IPCC, 2007. WGI AR4 - the physical science basis, in: Contribution of working group i to the fourth assessment report of the intergovernmental panel on climate change. Cambridge University Press, Cambridge, UK,. https://doi.org/10.1017/CBO9780511546013
Janssen, A.B.G., Arhonditsis, G.B., Beusen, A., others, 2015. Exploring, exploiting and evolving diversity of aquatic ecosystem models: A community perspective, Aquatic Ecology 49, 513–548.
Jickells, T.D., Baker, A.R., Chance, R., 2016. Atmospheric transport of trace elements and nutrients to the oceans, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 374, 20150286.
Johnston, D., Chandrapavan, A., Wise, B., Caputi, N., 2014. Assessment of blue swimmer crab recruitment and breeding stock levels in the peel-harvey estuary and status of the mandurah to bunbury developing crab fishery. Fisheries research report no. 258. Department of Fisheries, Western Australia.
Jouon, A., Douillet, P., Ouillon, S., Fraunie, P., 2006. Calculations of hydrodynamic time parameters in a semi-opened coastal zone using a 3D hydrodynamic model, Continental Shelf Research 26, 1395–1415. https://doi.org/10.1016/j.csr.2005.11.014
Kanaya, G., Uehara, T., Kikuchi, E., 2016. Effects of sedimentary sulfide on community structure, population dynamics, and colonization depth of macrozoobenthos in organic-rich estuarine sediments, Marine pollution bulletin 109, 393—401.
Kasai, A., Kurikawa, Y., Ueno, M., Robert, D., Yamashita, Y., 2010. Salt-wedge intrusion of seawater and its implication for phytoplankton dynamics in the yura estuary, japan, Estuarine, Coastal and Shelf Science 86, 408–414. https://doi.org/10.1016/j.ecss.2009.06.001
Kelsey, P., Hall, J., Kretschmer, P., Quiton, B., Shakya, D., 2011. Hydrological and nutrient modelling of the peel-harvey catchment, water science technical series. Report no. 33. Department of Water; Environment Regulation, Western Australia.
Knoppers, B., Kjerfve, B., Carmouze, J.P., 1991. Trophic state and water turn-over time in six choked coastal lagoons in brazil, Biogeochemistry 14, 149–166. https://doi.org/10.1007/BF00002903
Kraal, P., Burton, E.D., Bush, R.T., 2013a. Iron monosulfide accumulation and pyrite formation in eutrophic estuarine sediments, Geochimica et Cosmochimica Acta 122, 75—88.
Kraal, P., Burton, E.D., Rose, A.L., Cheetham, M.D., Bush, R.T., Sullivan, L.A., 2013b. Decoupling between water column oxygenation and benthic phosphate dynamics in a shallow eutrophic estuary, Environmental science & technology 47, 3114—3121.
Krumholz, O., 2019. Macrophyte communities in the Peel-Harvey Estuary: Historical trends and current patterns in biomass and distribution, Murdoch University PhD Thesis.
Kuhn, M., Tuladhar, D., Corner, R., 2011. Visualising the spatial extent of predicted coastal zone inundation due to sea level rise in south-west western australia, Ocean & Coastal Management 54, 796–806. https://doi.org/10.1016/j.ocecoaman.2011.08.005
Ladson, A., 2008. Hydrology: An Australian Introduction. Oxford University Press, Melbourne.
Lavery, P.S., McComb, A.J., 1991. Macroalgal-sediment nutrient interactions and their importance to macroalgal nutrition in a eutrophic estuary, Estuarine, Coastal and Shelf Science 32, 281–295. https://doi.org/10.1016/0272-7714(91)90021-3
Legović, T., Ẑutić, G., V., Viličié, D., 1994. Eutrophication in the Krka estuary, Marine Chemistry 46, 203–215. https://doi.org/10.1016/0304-4203(94)90056-6
Liu, W.C., Chan, W.T., 2016. Assessment of climate change impacts on water quality in a tidal estuarine system using a three-dimensional model, Water 8, 60. https://doi.org/10.3390/w8020060
Loneragan, N.R., Potter, I.C., Lenanton, R.C.J., Caputi, N., 1986. Spatial and seasonal differences in the fish fauna in the shallows of a large Australian estuary, Marine Biology 92, 575—586.
Lord, D.A., 1998. Dawesville channel monitoring programme. Water and Rivers Commission.
Macreadie, P.I., Jarvis, J., Trevathan-Tackett, S.M., Bellgrove, A., others, 2017. Seagrasses and macroalgae: Importance, vulnerability and impacts, Climate Change Impacts on Fisheries and Aquaculture: A Global Analysis (Wiley-Blackwell) 729—770.
Mahmoud, M., Liu, Y.Q., Hartmann, H., Stewart, S., Wagener, T., Semmens, D., Stewart, R., Gupta, H., Dominguez, D., Dominguez, F., Hulse, D., Letcher, R., Rashleigh, B., Smith, C., Street, R., Ticehurst, J., Twery, M., Delden, H. van, Waldick, R., White, D., Winter, L., 2009. A formal framework for scenario development in support of environmental decision-making, Environmental Modelling & Software 24(7), 798–808.
Manda, A.K., Giuliano, A.S., Allen, T.R., 2014. Influence of artificial channels on the source and extent of saline water intrusion in the wind tide dominated wetlands of the southern albemarle estuarine system (USA), Environmental Earth Sciences 71, 4409–4419. https://doi.org/10.1007/s12665-013-2834-9
Martinho, F., Nyitrai, D., Crespo, D., Pardal, M.A., 2015. Efficacy of single and multi-metric fish-based indices in tracking anthropogenic pressures in estuaries: an 8-year case study, Marine pollution bulletin 101, 153—162.
McComb, A.J., Atkins, R.P., Birch, P.B., Gordon, D.M., Lukatelich, R.J., 1981. Eutrophication in the Peel-Harvey estuarine system, western Australia, in: Estuaries and Nutrients. Springer, p. 323—342.
McComb, A.J., Humphries, R., 1992. Loss of nutrients from catchments and their ecological impacts in the Peel-Harvey estuarine system, Western Australia, Estuaries 15, 529.
McComb, A.J., Qiu, S., Lukatelich, R.J., McAuliffe, T.F., 1998. Spatial and temporal heterogeneity of sediment phosphorus in the Peel-Harvey estuarine system, Estuarine, Coastal and Shelf Science 47, 561—577.
McIlvin, M.R., Casciotti, K.L., 2011. Technical updates to the bacterial method for nitrate isotopic analyses, Analytical Chemistry 83, 1850—1856.
Monsen, N.E., Cloern, J.E., Lucas, L.V., Monismith, S.G., 2002. A comment on the use of flushing time, residence time, and age as transport time scales, Limnology and Oceanography 47, 1545–1553. https://doi.org/10.4319/lo.2002.47.5.1545
Morgan, B., Rate, A.W., Burton, E.D., Smirk, M.N., 2012. Enrichment and fractionation of rare earth elements in FeS-and organic-rich estuarine sediments receiving acid sulfate soil drainage, Chemical Geology 308, 60—73.
Paerl, H.W., Valdes, L.M., Peierls, B.L., Adolf, J.E., Harding, L.W., 2006. Anthropogenic and climatic influences on the eutrophication of large estuarine ecosystems, Limnology and Oceanography 51, 448–462. https://doi.org/10.4319/lo.2006.51.1_part_2.0448
Parfitt, R.L., Stevenson, B.A., Dymond, J.R., Schipper, L.A., Baisden, W.T., Ballantine, D.J., 2012. Nitrogen inputs and outputs for New Zealand from 1990 to 2010 at national and regional scales, New Zealand Journal of Agricultural Research 55, 241—262.
Patterson, J.J., Smith, C., Bellamy, J., 2013. Understanding enabling capacities for managing the “wicked problem” of nonpoint source water pollution in catchments: A conceptual framework, Journal of Environmental Management 128, 441–452.
Pearson, T.H., Rosenberg, R., 1978. Macrobenthic succession in relation to organic enrichment and pollution of the marine environment, Oceanography and Marine Biology: An Annual Review 16, 229–311.
Pedretti, Y.M., Kobryn, H.T., Sommerville, E.F., Wienczugow, K., 2011. Snapshot survey of the distribution and abundance of seagrass and macroalgae in the peel-harvey estuary from november/december 2009. Report to department of water. Report number MAFRL 11.
Perez-Dominguez, R., Maci, S., Courrat, A., Lepage, M., Borja, A., Uriarte, A., Neto, J.M., Cabral, H., Raykov, V.S., Franco, A., others, 2012. Current developments on fish-based indices to assess ecological-quality status of estuaries and lagoons, Ecological Indicators 23, 34—45.
Plummer, P., Taylor, M., 2001. Theories of Local Economic Growth: Concepts, Models and Measurements, Environment and Planning A 33, 219—236.
Plummer, P., Tonts, M., Martinus, K., 2014. Endogenous growth, local competitiveness and regional development: Western Australia’s Regional Cities, 2001-2011, Journal of Economic & Social Policy 16, 146.
Polasky, S., Carpenter, S.R., Folke, C., Keeler, B., 2011. Decision-making under great uncertainty: Environmental management in an era of global change. Trends in Ecology and Evolution, Trends in Ecology and Evolution 26, 398–404.
Potter, I.C., Chuwen, B.M., Hoeksema, S.D., Elliott, M., 2010. The concept of an estuary: A definition that incorporates systems which can become closed to the ocean and hypersaline, Estuarine, Coastal and Shelf Science 87, 497–500. https://doi.org/10.1016/j.ecss.2010.01.021
Potter, I.C., Loneragan, N.R., Lenanton, R.C.J., Chrystal, P.J., 1983a. Blue-green algae and fish population changes in a eutrophic estuary, Marine Pollution Bulletin 14, 228—233.
Potter, I.C., Loneragan, N.R., Lenanton, R.C.J., Chrystal, P.J., Grant, C.J., 1983b. Abundance, distribution and age structure offish populations in a Western Australian estuary, Journal of Zoology 200, 21—50.
Potter, I.C., Veale, L., Tweedley, J.R., Clarke, K.R., 2016. Decadal changes in the ichthyofauna of a eutrophic estuary following a remedial engineering modification and subsequent environmental shifts, Estuarine, Coastal and Shelf Science 181, 345–363.
Prestrelo, L., Monteiro-Neto, C., 2016. Before-after environmental impact assessment of an artificial channel opening on a south-western atlantic choked lagoon system, Journal of Fish Biology 89, 735–752. https://doi.org/10.1111/jfb.13012
Productivity Commission, 2017. Transitioning Regional Economies, Study Report. Canberra.
Raskin, P.D., 2005. Global scenarios: Background review for the Millennium Ecosystem Assessment, Ecosystems 8, 133–142.
Raymond, P.A., Saiers, J.E., Sobczak, W.V., 2016. Hydrological and biogeochemical controls on watershed dissolved organic matter transport: Pulse-shunt concept, Ecology 97, 5—16.
Richardson, N., Gordon, A., Muller, W., Whitfield, A., 2011. A weight-of-evidence approach to determine estuarine fish health using indicators from multiple levels of biological organization, Aquatic Conservation: Marine and Freshwater Ecosystems 21, 423—432.
Riekenberg, P.M., Oakes, J.M., Eyre, B.D., 2018. Short-term fate of intertidal microphytobenthos carbon under enhanced nutrient availability: a 13C pulse-chase experiment, Biogeosciences 15, 2873–2889.
Ritter, C., Montagna, P.A., Applebaum, S., 2005. Short-term succession dynamics of macrobenthos in a salinity-stressed estuary, Journal of Experimental Marine Biology and Ecology 323, 57–69. https://doi.org/10.1016/j.jembe.2005.02.018
Rogers, P., Hall, N., Valesini, F., 2010. Science strategy for the peel- harvey estuary. Prepared for the peel-harvey catchment council. Centre for Fish and Fisheries Research, Murdoch University, Murdoch WA.
Rose, T.H., Tweedley, J.R., Warwick, R.M., Potter, I.C., 2019. Zooplankton dynamics in a highly eutrophic microtidal estuary, Marine Pollution Bulletin 142, 433–451. https://doi.org/10.1016/j.marpolbul.2019.03.047
Rosenberg, R., Nilsson, H.C., Diaz, R.J., 2001. Response of benthic fauna and changing sediment redox profiles over a hypoxic gradient, Estuarine, Coastal and Shelf Science 53, 343—350.
Rossi, F., 2002. Dynamics of the polychaetes Desdemona ornata and Perinereis cultrifera and their resources of food in a Mediterranean mudflat, Marine Ecology 23, 285–296. https://doi.org/10.1046/j.1439-0485.2002.02792.x
Rumbold, C.E., Obenat, S.M., Spivak, E.D., 2015. Comparison of life history traits of Tanais dulongii (Tanaidacea: Tanaididae) in natural and artificial marine environments of the south-western Atlantic, Helgoland Marine Research 69, 231–242. https://doi.org/10.1007/s10152-015-0432-9
Rynne, P., Reniers, A., Kreeke, J. van de, MacMahan, J., 2016. The effect of tidal exchange on residence time in a coastal embayment, Estuarine, Coastal and Shelf Science 172, 108–120. https://doi.org/10.1016/j.ecss.2016.02.001
Sarre, G.A., Potter, I.C., 1999. Comparisons between the reproductive biology of black breamAcanthopagrus butcheri (Teleostei: Sparidae) in four estuaries with widely differing characteristics, International Journal of Salt Lake Research 8, 179—210.
Semeniuk, V., Wurm, P.A.S., 2000. Molluscs of the Leschenault Inlet estuary: Their diversity, distribution, and population dynamics, Journal of the Royal Society of Western Australia 83, 377–418.
Sheldon, J.E., Alber, M., 2006. The calculation of estuarine turnover times using freshwater fraction and tidal prism models: A critical evaluation, Estuaries and Coasts 29, 133–146.
Silberstein, R.P., Aryal, S.K., Durrant, J., Pearcey, M., Braccia, M., Charles, S.P., others, 2012. Climate change and runoff in south-western australia, Journal of Hydrology 475, 441–455. https://doi.org/10.1016/j.jhydrol.2012.02.009
Sipler, R.E., Bronk, D.A., 2015. Dynamics of dissolved organic nitrogen, in: Biogeochemistry of Marine Dissolved Organic Matter. Elsevier, p. 128—232.
Smith, I., Power, S., 2014. Past and future changes to inflows into perth (western australia) dams, Journal of Hydrology: Regional Studies 2, 84–96. https://doi.org/10.1016/j.ejrh.2014.08.005
Smith, P.E., Oakes, J.M., Eyre, B.D., 2016. Recovery of nitrogen stable isotope signatures in the food web of an intermittently open estuary following removal of wastewater loads, Estuarine, Coastal and Shelf Science 182, 170—178.
Snelgrove, P.V.R., 1998. The biodiversity of macrofaunal organisms in marine sediments, Biodiversity & Conservation 7, 1123–1132. https://doi.org/10.1023/A:1008867313340
Sullivan, L.A., Bush, R.T., Fyfe, D.M., 2002. Acid sulfate soil drain ooze: distribution, behaviour and implications for acidification and deoxygenation of waterways, in: Acid sulfate soils in Australia and China, Science Press 91—99.
Tagliapietra, D., Sigovini, M., Magni, P., 2012. Saprobity: A unified view of benthic succession models for coastal lagoons, Hydrobiologia 686, 15–28. https://doi.org/10.1007/s10750-012-1001-8
Taylor, R.B., Dean, R.G., 1974. Exchange characteristics of tidal inlets, Proceeding of 14th ASCE Coastal Engineering Conference (Copenhagen, Denmark), 2268–2289. https://doi.org/10.9753/icce.v14.132
Thanh, H.T., Tschakert, P., Hipsey, M.R., 2021. Examining fishery common-pool resource problems in the largest lagoon of Southeast Asia through a participatory systems approach, Socio-Ecological Practice Research 3, 131–152.
Thanh, H.T., Tschakert, P., Hipsey, M.R., 2020. Tracing environmental and livelihood dynamics in a tropical coastal lagoon through the lens of multiple adaptive Cycles, Ecology and Society 25(1), 31.
Tweedley, J.R., Hallett, C.S., Warwick, R.M., Clarke, K.R., Potter, I.C., 2016. The hypoxia that developed in a microtidal estuary following an extreme storm produced dramatic changes in the benthos, Marine & Freshwater Research 67, 327–341. https://doi.org/10.1071/MF14216
Tweedley, J.R., Warwick, R.M., Clarke, K.R., Potter, I.C., 2014. Family-level AMBI is valid for use in the north-eastern Atlantic but not for assessing the health of microtidal Australian estuaries, Estuarine, Coastal and Shelf Science 141, 85–96. https://doi.org/10.1016/j.ecss.2014.03.002
Tweedley, J.R., Warwick, R.M., Hallett, C.S., Potter, I.C., 2017. Fish-based indicators of estuarine condition that do not require reference data, Estuarine, Coastal and Shelf Science 191, 209–220.
Tweedley, J.R., Warwick, R.M., Valesini, F.J., Platell, M.E., Potter, I.C., 2012. The use of benthic macroinvertebrates to establish a benchmark for evaluating the environmental quality of microtidal, temperate southern hemisphere estuaries, Marine Pollution Bulletin 64, 1210–1221. https://doi.org/10.1016/j.marpolbul.2012.03.006
Valdemarsen, T., Kristensen, E., Holmer, M., 2010. Sulfur, carbon, and nitrogen cycling in faunated marine sediments impacted by repeated organic enrichment, Marine Ecology Progress Series 400, 37—53.
Valesini, F.J., Cottingham, A., Hallett, C.S., Clarke, K.R., 2017. Interdecadal changes in the community, population and individual levels of the fish fauna of an extensively modified estuary, Journal of Fish Biology 90, 1734–1767. https://doi.org/10.1111/jfb.13263
Valesini, F.J., Hallett, C.S., Hipsey, M.R., Kilminster, K.L., Huang, P., Hennig, K., 2019. Peel-harvey estuary, western australia, in: Coasts and estuaries: The future (edited by: Wolanski, E., Day, J.W., Elloitt, M., and Ramachandran, R.), Elsevier. https://doi.org/10.1016/C2017-0-00731-0
Wang, B., Hipsey, M.R., Oldham, C., 2020. ML-SWAN-v1: A hybrid machine learning framework for the concentration prediction and discovery of transport pathways of surface water nutrients, Geoscientific Model Development 13, 4253–4270.
Warwick, R.M., Clarke, K.R., 1993. Comparing the severity of disturbance: A meta- analysis of marine macrobenthic community data, Marine Ecology Progress Series 92, 221–231.
Watanabe, K., Kasai, A., Antonio, E.S., Suzuki, K., Ueno, M., Yamashita, Y., 2014. Influence of salt-wedge intrusion on ecological processes at lower trophic levels in the yura estuary, Japan, Estuarine, Coastal and Shelf Science 139, 67–77. https://doi.org/10.1016/j.ecss.2013.12.018
Weisberg, S.B., Ranasinghe, J.A., Dauer, D.M., Schaffner, L.C., Diaz, R.J., Frithsen, J.B., 1996. An estuarine benthic index of biotic integrity (B-IBI) for Chesapeake Bay, Estuaries 20, 149. https://doi.org/10.2307/1352728
Wells, F.E., Threlfall, T.J., 1982. Density fluctuations, growth and dry tissue production of Hydrococcus brazieri (Tenison Woods, 1876) and Arthritica semen (Menke, 1843) in Peel Inlet, Western Australia, Journal of Molluscan Studies 48, 310–320. https://doi.org/10.1093/oxfordjournals.mollus.a065653
Wells, N.S., Baisden, W.T., Horton, T., Clough, T.J., 2016. Spatial and temporal variations in nitrogen export from a New Zealand pastoral catchment revealed by stream water nitrate isotopic composition, Water Resources Research 52, 2840—2854.
Wells, N.S., Clough, T.J., Johnson-Beebout, S.E., Elberling, B., Baisden, W.T., 2019. Effects of denitrification and transport on the isotopic composition of nitrate (18O, 15N) in freshwater systems, Science of The Total Environment 651, 2228—2234.
Wells, N.S., Maher, D.T., Erler, D.V., Hipsey, M., Rosentreter, J.A., Eyre, B.D., 2018. Estuaries as sources and sinks of N2O across a land use gradient in subtropical australia, Global Biogeochemical Cycles 32, 877—894.
Welsh, W.D., Vaze, J., Dutta, D., Rassam, D., Rahman, J.M., Jolly, I.D., Wallbrink, P., Podger, G.M., Bethune, M., Hardy, M.J., 2013. An integrated modelling framework for regulated river systems, Environmental Modelling and Software 39, 81—102.
Whisson, C.S., Wells, F.E., Rose, T., 2004. The benthic invertebrate fauna of the Peel-Harvey Estuary of southwestern Australia after completion of the Dawesville Channel, Records of the Western Australian Museum 22, 81–90.
Whitehead, P.G., Wilby, R.L., Battarbee, R.W., Kernan, M., Wade, A.J., 2009. A review of the potential impacts of climate change on surface water quality, Hydrological Sciences Journal 54, 101–123. https://doi.org/10.1623/hysj.54.1.101
Whitfield, A.K., Elliott, M., 2002. Fishes as indicators of environmental and ecological changes within estuaries: a review of progress and some suggestions for the future, Journal of fish biology 61, 229—250.
Wildsmith, M.D., Rose, T.H., Potter, I.C., Warwick, R.M., Clarke, K.R., Valesini, F.J., 2009. Changes in the benthic macroinvertebrate fauna of a large microtidal estuary following extreme modifications aimed at reducing eutrophication, Marine Pollution Bulletin 58, 1250–1262. https://doi.org/10.1016/j.marpolbul.2009.06.008
Wildsmith, M.D., Valesini, F.J., Robinson, S.F., 2017. The value of enduring environmental surrogates as predictors of estuarine benthic macroinvertebrate assemblages, Estuarine, Coastal and Shelf Science. 197, 159–172. doi: 197, 159–172. https://doi.org/10.1016/j.ecss.2017.08.006
Wilson, C., Paling, E.I., Latchford, J.A., 1999. Macrophyte abundance, distribution and composition of the Peel-Harvey Estuary: comparisons before and after the opening of the Dawesville Channel (July 1985 to June 1999), Marine and Freshwater Research Laboratory, Environmental Science.
Xue, D., Baets, B.D., Cleemput, O.V., Hennessy, C., Berglund, M., Boeckx, P., 2012. Use of a Bayesian isotope mixing model to estimate proportional contributions of multiple nitrate sources in surface water, Environmental Pollution 161, 43—49.
Yeoh, D.E., Valesini, F.J., Hallett, C.H., 2019. Monitoring the fish fauna and ecosystem health of the Walpole and Nornalup Inlets Marine Park 2018/19. Report to the Department of Primary Industries and Regional Development. Murdoch University, Perth, Western Australia.
Zhang, L., Altabet, M.A., Wu, T., Hadas, O., 2007. Sensitive measurement of NH4+ 15N/14N (delta 15NH4+) at natural abundance levels in fresh and saltwaters, Analytical Chemistry 79, 5297—5303.
Zhu, Y., McCowan, A., Cook, P.L.M., 2017. Effects of changes in nutrient loading and composition on hypoxia dynamics and internal nutrient cycling of a stratified coastal lagoon, Biogeosciences 14, 4423–4433. https://doi.org/10.5194/bg-14-4423-2017