Understanding the dynamics of fish ecology and movements: implications for management of a temperate estuarine marine park Daniel Edward Yeoh BSc (Hons) Murdoch University This thesis is presented for the degree of Doctor of Philosophy of Murdoch University, Western Australia 2018 Declaration I declare that this thesis is my own account of my research and contains as its main content work which has not previously been submitted for a degree at any tertiary education institution. Daniel Edward Yeoh Abstract The overarching aim of this study was to provide a detailed ecological understanding of the fish fauna of a temperate microtidal estuary in south-western Australia (SWA), the Walpole-Nornalup Marine Park. Located in a global climate change hotspot, this largely unmodified and permanently-open system is the only marine park on the south coast of WA. Despite its small size, it has the highest recreational fishing activity in the bioregion, yet managers lack contemporary understanding of its fish fauna and the ability to detect limits of acceptable change. A multi-faceted monitoring approach combining surveys of fish assemblages and acoustic telemetry was used to address the following key objectives: (1) quantify spatio-temporal shifts in fish faunal composition, (2) assess changes in fish communities, populations and a fish-based index of ecosystem health since the last studies in the 1990s, and (3) track the detailed movements of key fishery species. This study is one of the few globally to characterise fish responses to natural and anthropogenic drivers at the individual, population, community and ecosystem levels. Various structural and functional attributes of fish assemblages were examined throughout the system between day and night, seasons and years from July 2014–May 2016. Forty-seven species from 29 families were recorded, placing this estuary among the most diverse in the region. Marine-associated species, many of fishery importance, dominated the composition. Most ichthyofaunal attributes differed between estuarine regions, day–night, seasons and years, reflecting mainly habitat preferences or, in the case of diel patterns, changes in fish activity and predator–prey interactions. Since the 1990s, marine and warmer-water species have increased in abundance, while larger benthic species have decreased. Size declines in fishery species were also detected. Ecological health of the deeper waters has deteriorated over time, while the reverse occurred in the shallows. These findings likely reflect the effects of accelerated warming and drying of the climate, combined with increased fishing activity. Acoustic tracking of Acanthopagrus butcheri, Chrysophrys auratus, Rhabdosargus sarba (Sparidae) and Platycephalus speculator (Platycephalidae) revealed marked differences in their estuarine-marine connectivity, intra-estuarine use and mobility. Drivers of these patterns, which were mixed among species, principally reflected spawning behaviours, habitat preferences, feeding modes and responses to water temperature and freshwater I flow. This is the first multi-species tracking study in a SWA estuary, and highlights their divergent estuarine use, vulnerability to fishing and shifts in niche overlap likely to occur with further climate change. The multiple fish assessment techniques at a range of organisational levels presented here provide a major contribution towards the refinement of robust faunal monitoring regimes, which are currently lacking in Australian estuarine management. Such regimes, combined with sound data on the environmental and social pressures on estuaries, are imperative for the effective management of estuarine ecosystems and their fisheries. II Contents ABSTRACT ..................................................................................................................... I CONTENTS .................................................................................................................. III LIST OF FIGURES ..................................................................................................... VI LIST OF TABLES .................................................................................................... XIII ACKNOWLEDGEMENTS ....................................................................................... XVI CHAPTER 1: GENERAL INTRODUCTION ............................................................. 1 1.1 THE ESTUARINE ENVIRONMENT ................................................................................ 1 1.2 FISHES IN ESTUARIES ................................................................................................ 2 1.3 ESTUARIES AND HUMANS: USES AND IMPACTS ......................................................... 3 1.4 MANAGEMENT OF ESTUARIES AND THEIR FISH STOCKS ............................................ 5 1.4 ESTUARIES OF SOUTH-WESTERN AUSTRALIA ............................................................ 7 1.5 WALPOLE-NORNALUP ESTUARY ............................................................................ 10 1.6 STUDY RATIONALE, OBJECTIVES AND THESIS STRUCTURE ...................................... 11 CHAPTER 2: HIERARCHICAL ENVIRONMENTAL FILTERS SHAPING THE FISH FAUNA OF THE WALPOLE-NORNALUP ESTUARY ............................... 13 2.1 INTRODUCTION ....................................................................................................... 13 2.2 METHODS ............................................................................................................... 17 2.2.1 Study area ...................................................................................................... 17 2.2.2 Fish faunal sampling ...................................................................................... 18 2.2.3 Measurement of water quality parameters .................................................... 20 2.2.4 Data analyses ................................................................................................. 20 2.3 RESULTS ................................................................................................................. 23 2.3.1 Physico-chemical water variables ................................................................. 23 2.3.2 Overall fish species abundances and guilds .................................................. 25 2.3.3 Regional, seasonal and interannual differences in nearshore fish communities ............................................................................................................ 31 2.3.4 Regional, seasonal and interannual differences in offshore fish communities ................................................................................................................................. 39 2.4 DISCUSSION ............................................................................................................ 44 2.4.1 How does the fish faunal diversity of the Walpole-Nornalup compare with that of other south-western Australian estuaries in different bioregions and with different mouth states? ............................................................................................ 44 2.4.2 How do intra-estuarine habitat filters shape the fish fauna of the Walpole- Nornalup Estuary? .................................................................................................. 51 2.4.3 How do environmental influences drive seasonal and interannual changes in the fish fauna of the Walpole-Nornalup Estuary? .................................................. 54 2.4.4 The importance of the estuary as a nursery for marine species, and particularly those of fishery importance ................................................................. 57 2.4.5 Conclusions .................................................................................................... 58 CHAPTER 3: DIEL SHIFTS IN THE STRUCTURE AND FUNCTION OF NEARSHORE FISH COMMUNITIES ...................................................................... 60 3.1 INTRODUCTION ....................................................................................................... 60 III 3.2 METHODS ............................................................................................................... 65 3.2.1 Study area ...................................................................................................... 65 3.2.2 Field sampling ................................................................................................ 65 3.2.3 Data analyses ................................................................................................. 66 3.3 RESULTS ................................................................................................................. 69 3.3.1 Diel changes in water quality parameters ..................................................... 69 3.3.2 Diel changes in total species abundances ...................................................... 69 3.3.3 Diel changes in fish abundance, species richness and taxonomic distinctness ................................................................................................................................. 71 3.3.4 Diel changes in species, guild and size composition ..................................... 72 3.4 DISCUSSION ............................................................................................................ 76 3.4.1 Diel changes in fish abundance, species richness and taxonomic distinctness ................................................................................................................................