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Shellfish reefs have been lost from bays and estuaries globally, including in the Swan-Canning Estuary in Western Australia. As part of a national program to restore the ecosystem services that such reefs once provided and return this habitat from near extinction, the mussel Mytilus galloprovincialis was selected for a large-scale shellfish reef construction project in this estuary. To assess the potential filtration capacity of the reef, estuary seston quality, mussel feeding behavior, and valve gape activity were quantified in the laboratory and field during winter and summer. In general, estuary water contained high total particulate concentrations (7.9–8.7 mg L−1). Standard clearance rates were greater in winter (1.9 L h−1; 17 °C) than in summer (1.3 L h−1; 25 °C), the latter producing extremely low absorption efficiencies (37%). Mussel valves remained open ~97% and ~50% of the time in winter and summer, respectively. They often displayed erratic behavior in summer, possibly due to elevated temperatures and the toxic microalgae Alexandrium spp. Despite numerous stressors, the reef, at capacity, was estimated to filter 35% of the total volume of the estuary over winter, incorporating 42.7 t of organic matter into mussel tissue. The reefs would thus make a substantial contribution to improving estuary water quality

Microtidal estuaries are prone to anthropogenic degradation, with natural features of those in south-western Australia making them more susceptible. However, the benthic ecological health of these systems is rarely assessed, despite the importance of the benthos and frequent application of benthic indices in estuaries elsewhere, particularly macrotidal systems in the northern hemisphere. The aim of this research was to assess the current status of the benthic macroinvertebrate community and its role in the function and management of the microtidal Peel-Harvey Estuary. After accounting for the effects of natural hydrological conditions (e.g. salinity, temperature), the benthic macroinvertebrate community was shown to respond to anthropogenic stress as represented by sediment condition (i.e. oxygenation, organic enrichment, mud content, sulphide presence), demonstrating its potential utility for assessing estuarine health. However, existing benthic indices commonly used in macrotidal estuaries (e.g. the multivariate AZTI Marine Biotic Index) yielded results inconsistent with sediment condition, demonstrating their limitations when applied to highly adaptive, stress-tolerant macroinvertebrate communities that are common in microtidal estuaries. A new multi-metric Estuarine Benthic Community Index was developed, following a multivariate approach to select community metrics that showed greater responses to sediment condition than natural stress. Overall, the benthic macroinvertebrate community in the Peel-Harvey Estuary was typically in good to fair health, with decreased health in the summer and deeper depositional areas. It is largely dominated by small-bodied, opportunistic species, and apparently retained in early succession due to chronic natural and anthropogenic stress. This was further reflected by the community’s limited impacts on solute fluxes of benthic metabolism, nutrient exchange and denitrification, with sediment condition being more influential. These fi

Estuaries are significant coastal environments and amongst the most productive ecosystems. However, anthropogenic activities have led to widespread degradation of estuaries and loss of ecosystem function. Eutrophication, a major driver for these changes, caused widespread loss of seagrass and significant blooms of macroalgae and phytoplankton. This study determined the spatial and temporal dynamics of macrophyte communities over a forty-year period (1978- 2018) in the Peel- Harvey Estuary, a hydrologically modified eutrophic estuary in south-western Australia. Analyses revealed a progressive decline in macroalgal biomass and an associated increase in seagrass biomass over the examined periods. The seagrass Ruppia became the dominant macrophyte in the system and expanded into previously unvegetated areas in the southern Harvey Estuary. The observed changes in macrophyte community composition were correlated with declining total nitrogen concentrations over time in those regions of the estuary furthest from the rivers. While these effects partly reflect improved water clarity and flushing of nutrients following the opening of an artificial channel to the ocean, they are likely also influenced by changes in river flow patterns caused by climate change. Although the overall seagrass expansion and decline in macroalgal biomass can be perceived as signals of improved estuary health, areas close to the river mouths remain exposed to higher nutrient loads. Significant accumulations of the green algae Willeella brachyclados (formerly Cladophora montagneana) in these areas underpin the potential vulnerability of the system to algal blooms and seagrass decline. Future research and monitoring is required to understand the potential threats to macrophyte communities in the Peel-Harvey Estuary from ongoing climate change.

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 shall

Maintaining the health of aquatic systems is an essential component of sustainable catchment management, however, degradation of water quality and aquatic habitat continues to challenge scientists and policy-makers. To support management and restoration efforts aquatic system models are required that are able to capture the often complex trajectories that these systems display in response to multiple stressors. This paper explores the abilities and limitations of current model approaches in meeting this challenge, and outlines a strategy based on integration of flexible model libraries and data from observation networks, within a learning framework, as a means to improve the accuracy and scope of model predictions. The framework is comprised of a data assimilation component that utilizes diverse data streams from sensor networks, and a second component whereby model structural evolution can occur once the model is assessed against theoretically relevant metrics of system function. Given the scale and transdisciplinary nature of the prediction challenge, network science initiatives are identified as a means to develop and integrate diverse model libraries and workflows, and to obtain consensus on diagnostic approaches to model assessment that can guide model adaptation. We outline how such a framework can help us explore the theory of how aquatic systems respond to change by bridging bottom-up and top-down lines of enquiry, and, in doing so, also advance the role of prediction in aquatic ecosystem management.

Visitors who exhibit place attachment often demonstrate greater concern regarding how a place is managed. However, the extent to which the dimensions of attachment are related to management preferences has not been sufficiently investigated. Place attachment of visitors to coastal campsites along the southern Ningaloo coastline of northwestern Australia and its relation with management preferences were examined via an onsite survey. The relation was investigated using a suite of routines in the non-parametric multivariate statistics package PRIMER v6, providing the first example of the use of these types of statistical approaches in place research. Place attachment was measured using the dimensions of Place Identity, Place Dependence, and Everybody's Happy (a new, affective-based dimension). Within each dimension, significantly different groups of visitors were identified based on differences in their responses to the place attachment survey items. This was achieved using hierarchical agglomerative cluster analysis in conjunction with a Similarity Profile (SIMPROF) test. Subsequent analysis using the BVSTEP procedure showed that the pattern of differences among visitors in their responses to place attachment items produced significant though weak correlations with their level of support for various management actions. The authors conclude with a discussion of the implications of the results for future research on place and associated preferences for management actions.

Estuaries are especially vulnerable to the impacts of climate change because changes in climatic and hydrologic variables that influence freshwater and marine systems will also affect estuaries. We review potential impacts of climate change on Australian estuaries and their fish. Geographic differences are likely because southern Australian climates are predicted to become warmer and drier, whereas northern regions may see increased precipitation. Environmental factors, including salinity gradients, suspended sediment, dissolved oxygen and nutrient concentrations, will be influenced by changing freshwater input and other climate variables. Potential impacts will vary depending on the geomorphology of the estuary and the level of build-up of sand bars across estuarine entrances. Changes to estuarine fish assemblages will depend on associated changes to salinity and estuarine-mouth morphology. Marine migrants may be severely affected by closure of estuarine mouths, depending on whether species ‘must’ use estuarine habitat and the level of migratory v. resident individuals. Depending on how fish in coastal waters locate estuaries, there may be reduced cues associated with estuarine mouths, particularly in southern Australia, potentially influencing abundance. In summary, climate change is expected to have major consequences for Australian estuaries and associated fish, although the nature of impacts will show significant regional variation.

The work for this thesis was undertaken in Broke Inlet, a seasonally-open estuary on the south coast of Western Australia and the only estuary in that region which is regarded as “near-pristine” (Commonwealth of Australia, 2002). The only previous seasonal studies of the environmental and biotic characteristics of this estuary involved broad-based descriptions of the trends in salinity, temperature and ichthyofaunal characteristics at a limited number of sites. Furthermore, no attempt has been made to identify statistically the range of habitats present in the nearshore and offshore waters of this system, and the extents to which the characteristics of the fish and benthic invertebrate faunas are related to habitat type. These types of data provide not only reliable inventories of the habitat and faunal characteristics of Broke Inlet, but also a potential basis for predicting the likely impact of anthropogenic and climatic changes in Broke Inlet in the future. The main aims of this thesis were as follows. (1) To use the method of Valesini et al. (2010), which employs enduring environmental characteristics, to identify quantitatively the range of habitats present throughout the nearshore and offshore waters of Broke Inlet. The enduring environmental characteristics represent three broad categories, i.e. the location of any site in terms of its proximity to marine and freshwater sources, the degree of exposure to wave activity and the type of substrate and/or submerged vegetation. (2) To test the hypothesis that the species richness, density, diversity and species compositions of the fish and benthic macroinvertebrate faunas differ among habitat types, seasons and, in the case of the fish fauna, also years. (3) To test the hypothesis that the pattern of relative differences among habitat types, as exhibited by their faunal compositions, is correlated with that defined by their (i) enduring environmental characteristics and (ii) non-enduring environmental characteristi

The overall aim of this thesis was to develop an approach for constructing and validating a fish-based, multimetric index for assessing the ecological health of estuaries in south-western Australia, and to apply that approach to the large Swan Estuary, which has been subjected to substantial anthropogenic pressures. The indices developed for nearshore and offshore waters are the first to be produced for Western Australian estuaries. They deliver a reliable, practical and cost-effective method for quantifying the status of estuarine health, thus providing managers with a sound basis for preventative management actions and a means for communicating ecosystem health implications to the wider public. An extensive range of potential fish community characteristics (metrics) were initially tested for their suitability for incorporation into the indices. These metrics included various measures of species composition, diversity and abundance, trophic and functional aspects of the assemblage, i.e. the contributions of different feeding and lifehistory guilds and, where relevant, sentinel species. An a priori hypothesis was formulated for each candidate metric, reflecting its predicted response to increasing ecosystem degradation. Two different approaches were trialled to identify the subset of metrics that were most sensitive to changes in environmental integrity and thus most appropriate for inclusion in an index of ecosystem health. The first approach sought to identify those metrics that showed the strongest responses to spatial differences in the quality of physical habitat, as quantified using a novel and independent measure of habitat degradation. Habitat quality was thus assessed at 136 nearshore sites throughout the estuary in spring 2007, using rapid visual survey techniques to assign scores for each of six habitat quality metrics. Scores for all physical habitat metrics were then summed to produce an overall habitat quality index score for each site. The results of

The overarching aim of this thesis was to describe the ecology of the assemblages of free-living nematodes in the sediments of nearshore marine and estuarine waters on the microtidal lower west coast of Australia. The thesis also provides descriptions of ten previously undescribed species as well as develops and tests a habitat classification scheme for the Swan River Estuary using these biotic assemblages. The first section of my thesis has determined the ways in which the characteristics of the nematode assemblages in nearshore marine waters along the microtidal lower west coast of Australia are related to habitat type, time of year and shore-perpendicular zones. Three habitat types, which had previously been identified on the basis of a suite of enduring environmental characteristics, could be broadly described as highly sheltered from wave activity and containing dense seagrass (habitat type 1), moderately sheltered from wave activity and with sparse seagrass (habitat type 2) and relatively exposed to wave activity and with no seagrass (habitat type 6). Sampling in five consecutive seasons yielded > 15 000 nematodes, representing 75 species. The number of species and densities in habitat type 1, and particularly those in its subtidal zone, were far greater than those in the other two habitat types. Both of these biotic variables underwent marked seasonal changes, declining to low levels during winter. The compositions of the assemblages differed significantly among the three habitat types, with the differences between habitat types 1 and 6 being particularly marked. Paracomesoma sipho, Dichromadora sp., Marylynnia annae and Pomponema sp., which, on the basis of their buccal cavity morphology, are assumed to feed primarily on benthic diatoms, were particularly abundant at the most sheltered habitat type, whereas Gonionchus australis, Theristus sp. and Bathylaimus australis, which are assumed to be deposit feeders, were relatively abundant at the most highly expos

The following four broad aims were addressed in this study. (1) To ascertain whether the characteristics of the benthic macroinvertebrate assemblages within the different nearshore marine habitat types identified by Valesini et al. (2003) on the lower west coast of Australia differ significantly, and whether the pattern of those spatial differences matches those among the environmental characteristics that were used to distinguish those habitat types; (2) To develop a quantitative approach for classifying nearshore habitats in estuarine waters that employs readily-available data for a range of enduring environmental characteristics, and to use that approach to classify the various habitat types present in nearshore waters of the Swan-Canning Estuary on the lower west coast of Australia; (3) To test the hypothesis that the characteristics of the benthic macroinvertebrate assemblages in the in the Swan-Canning Estuary differ significantly among nearshore habitat types, and that the pattern of those differences matches that among the environmental characteristics used to distinguish those habitat types and (4) To test the hypothesis that, as a result of environmental changes in the Swan-Canning Estuary, the characteristics of the benthic macroinvertebrate assemblages at various habitats in this estuary in 1986/7 differ from those in 2003/4. To address the first aim, benthic macroinvertebrates were sampled seasonally for one year in the subtidal waters and intertidal zone (upper and lower swash zones) at the six nearshore habitat types that were identified by Valesini et al. (2003) on the lower west coast of Australia. The habitat types, which differed mainly in the extent of their exposure to wave activity and whether seagrass and/or nearshore reefs were present, had been distinguished quantitatively using values for a suite of seven statistically-selected enduring environmental characteristics. The faunal samples yielded a total of 121 species representing eight phyla

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 (5), 1357-1373. Available here