Drivers of spatial and temporal movement patterns of Acanthopagrus butcheri through an estuarine surge barrier Submitted by Richelle McCormack This thesis is presented for the degree of Bachelor of Science Honours. College of Science, Health, Engineering and Education, Murdoch University 2019 Declaration I declare this thesis is my own account of my research and contains as its main content work which has not been previously submitted for a degree at any tertiary education institution. Richelle McCormack ii Acknowledgements I would like to extend a very special thank you to all my supervisors. Dr Stephen Beatty for all his expertise and knowledge on freshwater ecosystems and statistics; Dr James Tweedley for his expert knowledge on the Vasse-Wonnerup Estuary and thorough editing of all my work; and Dr Alan Cottingham for his expert knowledge on all things Black Bream, south-west Australian estuaries and for teaching me the ropes on catch and release and PIT tagging of fish in the middle of the night on board a little rickety dinghy in Busselton. I feel so lucky to have had three amazing academics by my side throughout my Honours experience, who have worked collaboratively to make this as much an enjoyable and educational experience as Honours can be. They all dedicated so much time and effort in covering my drafts in red ink and meeting with me for countless hours, and I am so grateful for their dedication. My supervisors also introduced me to a wealth of professionals who aided in my research. Thank you to Tom Ryan for his technical assistance and initial set up of the PIT antenna system. I extend a lot of gratitude to GeoCatch and Department of Water and Environmental Regulation (DWER) and the Water Corporation for the hydrological data and Bureau of Meteorology (BoM) for the environmental data without which this project would not have been possible. The fieldwork components of this project were also funded by DWER (IRMA 17379) with support from GeoCatch, so another massive thanks for that. My sincere gratitude goes to Karl Pomorin Karltek whose technology in conjunction with the PIT system made tracking fish from the comfort of my lounge room possible. Thank you to the Busselton and Molloy Senior high schools for assisting in the collection of in situ data, and the wider Busselton community for showing a genuine interest in the health and management of the Vasse-Wonnerup Estuary. The study was conducted under Murdoch University Animal Ethics Committee permit RW2793/15 and Department of Primary Industries and Regional Development (Fisheries) Exemption 2902. I acknowledge the Noongar people who are the Traditional Custodians of the land on which my research took place. iii To the great friends I’ve made through the last year and a half that have provided moral support, motivation and just great banter- Elysia Tingey and Georgina Stagg, it’s been comforting knowing we’ve all been in the same boat, so thank you so much! Last but definitely not least, a huge thank you and deepest appreciation and love to my incredible partner Tyson Addicoat who has supported me in every way throughout this project. His emotional support, positivity and ability to put up with my sleep deprivation and stress induced moods in particular has been nothing short of heroic. To all my friends and family that I have had to cancel plans on and have not seen for a while, thank you for your understanding, and I cannot wait to make up for lost time in seeing you all now that my studies are complete... until next time! iv Abstract Coastal and estuarine environments are popular sites for human settlement, yet they are among the most vulnerable to changing climate and extreme weather events such as rising sea level and storm surges. Storm surge barriers have been installed in numerous estuaries around the world to mitigate flooding risk. However, these structures have numerous deleterious impacts on ecological connectivity by restricting flow and fragmenting habitats, thus preventing fishes from accessing preferred spawning, nursery and feeding areas. Despite the ecological impact of estuarine surge barriers being well recognised, few studies have investigated their impact on obligate estuarine fishes; particularly at the individual level. The highly degraded Vasse-Wonnerup Estuary in south-western Australia has suffered regular mass fish kills, and fish gates were installed on the storm surge barriers to enable two-way fish passage in times of poor water quality. However, the majority of recent fish kills have occurred immediately upstream of the Vasse Surge Barrier (VSB) suggesting the gates have been ineffective in facilitating movement. The sparid Acanthopagrus butcheri has been particularly impacted by these fish kills. Due to its large body size, life-history characteristics and socio-economic importance in southern Australia, this obligate estuarine species is ideal to investigate how fish passage through the VSB may be influenced by prevailing environmental conditions. The fine-scale movement patterns of passive integrated transponder (PIT) tagged A. butcheri were monitored through the VSB using a custom designed system between 20th March 2017 and 31st May 2018. Passage data were analysed together with a suite of hydrological and environmental variables using generalised additive mixed models to determine the drivers of fish approaches (i.e. those detected at the downstream site of the fish gate without subsequently passing through) and the daily and hourly upstream and downstream passages through the fish gate. Daily approaches of A. butcheri to the VSB were typically greatest during September-December and April-May. As the species is known to spawn in July-October in the system, the increase in PIT detections in spring may have been partially associated v with an adult upstream migration. However, the key spawning site for the species is known to occur in another region of the system (i.e. the ‘Deadwater’ region) rather than habitats upstream of the VSB. This fact, along with the increase in detections at the VSB that occurred during April-May outside of the spawning period, suggests that the peaks in detections at the VSB may have been attributed to high localised migration, rather than representing spawning activity. Hourly upstream and downstream passages through the fish gate were nocturnal and crepuscular, respectively. Downstream passages were also associated with declines in dissolved oxygen concentrations in the upstream habitats; suggesting that A. butcheri was seeking to escape poor water quality. However, the hourly and daily upstream and downstream passages of A. butcheri were also strongly associated with times of minimal flow velocity within the fish gate that occurred when water levels equalised on the upstream and downstream sides of the VSB. Therefore, while the species appeared to be avoiding poor water quality by passing through the fish gate, it appeared this could only occur during certain hydrological conditions. This likely limited its ability to freely escape from times of poor water quality, thus explaining the periodic fish kills that occur mostly upstream of the VSB. These findings have clear implications for the management of the VSB and also instream barriers in other systems that house A. butcheri. A key recommendation for the future management of the VSB is to automate the fish gate operation so it opens during times of upstream and downstream water equalisation. This would maximise fish passage opportunities and simultaneously prevent salt-water intrusion upstream prevents stratification and associated hypoxia and toxic algal blooms. Given the projected increase in sea level rise and decrease in rainfall in south- western Australia, and indeed many parts of the world, associated with climate change, the construction of storm surge barriers is becoming more prevalent. This study highlights the need to understand the movement patterns and life-history requirements of resident estuarine species to maintain connectivity to critical habitats. vi Contents Acknowledgements ..................................................................................................... iii Abstract ........................................................................................................................ v 1. Introduction ............................................................................................................. 1 1.1. Estuaries and their fish faunas ....................................................................................... 1 1.2. Threats to estuaries ....................................................................................................... 3 1.3. Instream barriers ........................................................................................................... 5 1.4. South-western Australian estuaries ............................................................................... 7 1.5. Acanthopagrus butcheri................................................................................................. 8 1.6. Aims and hypotheses ..................................................................................................... 9 2. Materials and Methods .......................................................................................... 10 2.1. Study site......................................................................................................................10 2.2. Surge barrier and fish fauna ..........................................................................................13