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Identifying Water Quality and Ecosystem Health Threats to the Torres Strait and Far Northern GBR Arising from Runoff of the Fly River

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Identifying Water Quality and Ecosystem Health Threats to the Torres Strait and Far Northern GBR Arising from Runoff of the Fly River Final Report Identifying water quality and ecosystem health threats to the Torres Strait and Far Northern GBR arising from runoff of the Fly River Jane Waterhouse, Caroline Petus, Scott Bainbridge, Simone C. Birrer, Jon Brodie, Anthony C. Chariton, Katherine A. Dafforn, Johanna E. Johnson, Emma L. Johnston, Yanfang Li, Janice Lough, Flavio Martins, Dominique O’Brien, Dieter Tracey, Eric Wolanski Identifying water quality and ecosystem health threats to the Torres Strait and Far Northern GBR arising from runoff of the Fly River Jane Waterhouse1, Caroline Petus1, Jon Brodie2, Scott Bainbridge3, Eric Wolanski1, Katherine A. Dafforn4, Simone C. Birrer5, Janice Lough3, Dieter Tracey1, Johanna E. Johnson6,7, Anthony C. Chariton4, Emma L. Johnston5, Yanfang Li8, Flavio Martins9, Dominique O’Brien1 1 TropWATER, James Cook University, Townsville, Australia 2 Centre of Excellence for Coral Reef Studies, James Cook University, Australia 3 Australian Institute of Marine Science, Townsville, Australia 4 Macquarie University, Sydney 5 University of New South Wales, Sydney 6 School of Marine and Tropical Biology, James Cook University, Australia 7 C2O Consulting, Cairns, Australia 8 Yantai Institute of Coastal Zone Research, Shandong Sheng, China 9 University of Algarve, Faro, Portugal Supported by the Australian Government’s National Environmental Science Program Project 2.2.1 Identifying the water quality and ecosystem health threats to the high diversity Torres Strait and Far Northern GBR from runoff from the Fly River © James Cook University, 2018 Creative Commons Attribution Identifying the water quality and ecosystem health threats to the high diversity Torres Strait and Far Northern GBR from runoff from the Fly River is licensed by the James Cook University for use under a Creative Commons Attribution 4.0 Australia licence. For licence conditions see: https://creativecommons.org/licenses/by/4.0/ National Library of Australia Cataloguing-in-Publication entry: 978-1-925514-27-8 This report should be cited as: Waterhouse, J., Petus, C., Brodie, J., Bainbridge, S., Wolanski, E., Dafforn, K.A., Birrer, S.C., Lough, J., Tracey, D., Johnson, J.E., Chariton, A.C., Johnston, E.L., Li, Y., Martins, F., O’Brien, D. (2018) Identifying water quality and ecosystem health threats to the Torres Strait and Far Northern GBR from runoff of the Fly River. Report to the National Environmental Science Program. Reef and Rainforest Research Centre Limited, Cairns (162pp.). Published by the Reef and Rainforest Research Centre on behalf of the Australian Government’s National Environmental Science Program (NESP) Tropical Water Quality (TWQ) Hub. The Tropical Water Quality Hub is part of the Australian Government’s National Environmental Science Program and is administered by the Reef and Rainforest Research Centre Limited (RRRC). The NESP TWQ Hub addresses water quality and coastal management in the World Heritage listed Great Barrier Reef, its catchments and other tropical waters, through the generation and transfer of world-class research and shared knowledge. This publication is copyright. The Copyright Act 1968 permits fair dealing for study, research, information or educational purposes subject to inclusion of a sufficient acknowledgement of the source. The views and opinions expressed in this publication are those of the authors and do not necessarily reflect those of the Australian Government. While reasonable effort has been made to ensure that the contents of this publication are factually correct, the Commonwealth does not accept responsibility for the accuracy or completeness of the contents, and shall not be liable for any loss or damage that may be occasioned directly or indirectly through the use of, or reliance on, the contents of this publication. Cover photographs: Jane Waterhouse This report is available for download from the NESP Tropical Water Quality Hub website: http://www.nesptropical.edu.au Identifying the water quality and ecosystem health threats to the Torres Strait from the Fly River CONTENTS Contents .................................................................................................................................. i List of Tables ......................................................................................................................... iii List of Figures ........................................................................................................................ iv Appendices: List of Tables .................................................................................................. viii Appendices: List of Figures ................................................................................................... ix Acronyms and Abbreviations ................................................................................................. xi Acknowledgements ............................................................................................................. xiii Executive Summary ............................................................................................................ xiv 1. Introduction .................................................................................................................... 1 1.1 Background ............................................................................................................. 1 1.2 Project objectives .................................................................................................... 2 2. The Torres Strait region.................................................................................................. 4 2.1 Regional overview ................................................................................................... 4 2.2 The Fly River and its catchments ............................................................................ 5 2.3 Ecological features of the region ............................................................................. 6 2.4 Current status, threats and pressures to ecosystems .............................................. 9 2.4.1 Status and trends of Torres Strait ecosystems potentially influenced by the Fly River ................................................................................................................ 9 2.4.2 Pressures and threats: current and future .......................................................15 3. Existing evidence of the extent of influence of Fly River discharges in the Torres Strait region ............................................................................................................................17 3.1 Water quality monitoring in the Torres Strait ...........................................................17 3.2 The 2014 in-situ monitoring of dissolved metals .....................................................19 3.3 Assessment of oysters for the bioaccumulation of metals ......................................23 3.4 Potential impacts of increased sediment and trace metal inputs .............................23 4. Results from this study ..................................................................................................27 4.1 Coral cores .............................................................................................................27 4.1.1 Overview of methods and results ....................................................................27 4.1.2 Recommendations ..........................................................................................28 4.2 Hydrodynamic modelling ........................................................................................29 4.2.1 Overview of methods and results ....................................................................30 4.2.2 Recommendations ..........................................................................................35 4.3 Remote sensing analysis .......................................................................................35 4.3.1 Overview of methods and results ....................................................................37 i Waterhouse et al. 4.3.2 Recommendations ..........................................................................................41 4.4 In-situ continuous loggers ......................................................................................42 4.4.1 Overview of methods and results ....................................................................43 4.4.2 Recommendations ..........................................................................................50 4.5 Salinity monitoring ..................................................................................................51 4.5.1 Overview of methods and results ....................................................................51 4.5.2 Recommendations ..........................................................................................55 4.6 Water quality exposure assessment .......................................................................56 4.6.1 Overview of methods and results ....................................................................57 4.7 Testing correlations between water quality monitoring datasets .............................71 4.7.1 Overview of methods and results ....................................................................71 4.8 Gene sequencing in sediment samples ..................................................................77 4.8.1 Overview of methods and results ....................................................................78
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