Academic literature on the topic 'Swan-Canning Estuary'

Although medusae of the scyphozoan Phyllorhiza punctata are abundant in the Swan-Canning estuary during summer, they are absent when surface waters are dominated by low-salinity runoff water following winter rains. In the laboratory, scyphistomae of P. punctata are shown to survive in conditions of temperature and salinity that occur in the estuary during winter in waters deeper than 5 m. It is postulated that areas of deep water provide a winter refuge for scyphistomae and that asexual production of both ciliary buds and ephyrae enables rapid growth of the P. punctata population in the spring of each year.

In February 2000 the Swan-Canning estuary in Western Australia experienced a record bloom of the toxic cyanobacteria Microcystis aeruginosa. At its height, concentrations of M. aeruginosa reached integrated water column cell counts of 15,000/ml and formed bright green scums in sheltered bays, where counts of 130 million cells/ml were recorded. Due to public health concerns parts of the river were closed from 10 to 22 February 2000. Two unseasonably large summer rain events in early and late January 2000 created conditions for the bloom. Freshwater runoff, estimated at 270 GL, was enough to fill the Swan-Canning estuary five times over and brought with it high levels of nutrients, mainly nitrogen (>2.0mg/L TN) and phosphorus (>0.15mg/L TP). A number of methods to reduce bloom accumulations were tried, including an attempt to increase the salinity of the surface water above the critical 10 ppt level for Microcystis; using a bentonite clay and poly-aluminium chloride mixture to flocculate and sink the algae; and sucking up scums using oil spill equipment. Over 900 tonnes of M. aeruginosa were removed and safely disposed using sewage treatment facilities. The bloom collapsed when the freshwater flush subsided and seawater intrusion from the Indian Ocean re-established itself, raising the salinities above the tolerance of Microcystis.

Artificial oxygenation has been used for two summer periods to improve the water quality of the Canning River in Perth, Western Australia. The project is part of the Swan Canning Cleanup Program, which aims to reduce the frequency and severity of nuisance and toxic algal blooms in the Swan-Canning estuary. The trials have proved that oxygenation has increased the dissolved oxygen concentrations in the water column, particularly in the bottom waters where dissolved oxygen concentrations are frequently below a critical level of three milligrams per litre. Oxygenation has had a positive impact on nutrient concentrations in the water column and nitrogen cycling processes. Reductions in nutrient concentrations were highlighted by drops in ammonium and total phosphorus concentrations of 97% and 64% following the recommencement of oxygenation after a plant shutdown. Results of a microbiological study combined with the data analysis indicate that the number of nitrifying microbes have increased due to oxygenation. However, comparisons between oxygenated and control areas were inconclusive about the ability of the oxygenation plant to reduce total nitrogen and phosphorus levels. This could be explained by factors such as spatial variability, water flow during the trials and measurement limitations in the monitoring program. Future work will concentrate on assessing the impact of the oxygenation plant on nutrient concentrations.

Large extents of shellfish reefs have become degraded around the world as a result of anthropogenic activities to the point where such reefs are functionally extinct in some regions. Due to the ecosystem services provided by these biogenic habitats, there has recently been a concerted effort to restore shellfish reefs, particularly in Australia. While oysters have traditionally been used as a candidate species, the Mediterranean Mussel Mytilus galloprovincialis is gaining popularity and provides a similar suite of ecosystem services to oysters. As part of a pilot program, shellfish habitats, each comprising translocated M. galloprovincialis seeded onto 100 wooden stakes, were deployed at three sites in Melville Water in the Swan-Canning Estuary (Western Australia). The aims of this study where to; 1) investigate the mortality, body condition and growth of the translocated M. galloprovincialis; 2) compare the characteristics of fish fauna at the shellfish reef habitats and nearby unstructured (control) habitats and 3) determine the benthic macroinvertebrate and tunicate species associated with the shellfish habitat. The mortality of M. galloprovincialis was high at all three sites. This was attributed to poor environmental conditions in offshore waters of Melville Water, compounded by stress associated with translocation, their spawning activity, and fouling by ascidians. Seasonally adjusted von Bertalanffy growth models best explained the growth of M. galloprovincialis and growth was rapid, with individuals attaining ~50 mm within their first year. This is likely due to the high phytoplankton availability in the Swan-Canning Estuary. The shellfish habitats harboured a significantly different fish faunal composition compared to nearby unstructured habitats (sandy areas), with many species observed only at shellfish sites or in greater densities. The increased abundances of zoobenthivores on the shellfish habitats suggest they are utilising the invertebrate prey communities associated with the structure as a food source. The invertebrate community varied spatially among the three sites and over time. A suite of non-native ascidians rapidly colonised the stakes along with the mussels, which, in turn, supported many small crustaceans. Given the importance of shellfish restoration globally, and the aim to undertake large-scale projects to provide such habitats in south-western Australian estuaries, the results of this study will increase the understanding of the biology of M. galloprovincialis and help elucidate how faunal communities respond and utilise shellfish habitats. The results of this pilot study will assist in the planning of future mussel reef restoration projects, in particularly those under development in southern Australia.

This study documented the macroalgal assemblages of the Swan-Canning Estuarine System (SCES) over a two year period, and the influences of several environmental parameters on the assemblages. In addition, the Impacts of unattached macroalgal accumulations on benthic nutrient fluxes and microbial communities were investigated. Benthic macroalgal assemblages and physico-chemical regimes were monitored in the SCES, to determine temporal and spatial changes in macroalgal communities and the influence of environmental factors in these changes. Physico-chemical regimes demonstrated strong seasonal changes, which revolved around the onset and cessation of freshwater flows in winter (May to September). In the months after freshwater flows, strong spatial variability in physico-chemical profiles was observed. However, by summer the system was essentially marine. Macroalgal biomass and species richness was lowest in winter. Species number was maximal during periods of greatest hydrological variability in the estuary (spring and autumn). It may be inferred from results of statistical analyses that substrate type (i.e. hard/soft) and waterflow were the most Influential factors over temporal and spatial distribution of macroalgal species in the SCES. These factors ware reflected by the patchiness of macroalgal distribution in the system- attached macroalgal species distributed unevenly according to availability of limited hard substrate and presence/absence of unattached macroalgal species corresponding to seasonal freshwater flows. One species, Gracileria comosa, dominated macroalgal biomass and was the most widespread species and commonly occurred as extensive, unattached accumulations. As G. comosa was the most abundant unattached macroalga, accumulations of this species were investigated to determine the characteristics and behaviour or accumulations in the Swan-Canning Estuarine System. Accumulations were characterised by seasonally measuring height and biomass of accumulations in three regions or the estuarine system over one year. The height of accumulations was generally between 5 and 25cm, regardless of water depth, location, or season. Biomass was highly variable, but generally between 100 and 500 dw/m2 . The persistence of macroalgal accumulations was monitored at 28 sites within 10 estuarine regions, over a three month period, during which the first freshwater flows were recorded. Accumulations persisted between one week and one month, depending on the region, with accumulations persisting for longer periods in areas of low flow such as embayments and the regulated Canning River, and for shorter periods In regions of higher flow such as the channalised Swan River. Field and laboratory studies were performed to determine If the presence of G. comosa accumulations had an Impact on sediment-water nutrient exchange. Field studies established that accumulations affected benthic nutrient fluxes within a 24 hour period. However, this effect was site-dependent, occurring at an estuarine site of relatively high sediment organic content, but not at a site of relatively low sediment organic. Diurnal changes in water quality inside algal accumulations corresponded to photosynthetic/respiratory activity of the macroalgae - most notably, Increases In orthophosphate and ammonium fluxes from the sediment after approximately 8h of darkness. Since this effect was on time scales less than the period of persistence (weeks to months), It was concluded that macroalgal accumulations have an impact on benthic nutrient fluxes from sediments of relatively high organic content in the system. Laboratory studies investigated the effect of depth and density of an algal layer on sediment- water nutrient exchange. The experimental results concurred with field observations; water column concentrations of inorganic nutrients were significantly higher in sediment cores overlain by an algal layer over a 7 day period. In addition, Inorganic nutrient concentrations increased With Increasing height of the layer and ammonium concentrations increased with increasing density of the algal layer. Additional laboratory experiments tested the effect of an algal layer on sediment denitrification rates, and the composition and distribution of benthic microbial populations, Benthic nitrogen (N2) release rates were low irrespective of the presence of macroalgae and sediment types (less than 1mmo N/m2/d). However, release rates were significantly higher in sediment cores covered by algae than in comparable bare sediment cores, provided the algal layer was relatively high (5cm in height} and sediment organic content was high. The presence of an algal layer did not have a significant effect on the composition or distribution of microbes in the sediment. In all cases, microbial populations contained relatively few denitrifiers/nitrate reducers compared to nitrifiers and ammonifiers. High ammonium release rates from the sediment to the water column, and the low release rates of elemental nitrogen, suggested that even II the nitrate reducing bacteria were active they were not reducing nitrate to nitrogen, suggesting the possibility of Dissimilatory Nitrate Reduction to Ammonium (DNRA). Subsequent analysis confirmed that the nitrate reducers were reducing nitrate to nitrite, a result compatible with the hypothesis that the main microbial processes occurring were ammonification, nitrification, and DNRA, but not denitrification. These processes, regardless of the presence of a benthic algal layer, contribute to high ammonium flux rates from the sediment and provide a mechanism of internal inorganic nitrogen regeneration. In conclusion, this study has established that unattached macroalgal accumulations are a prominent component of the macroatgal community in the Swan-Canning Estuarine System. Accumulations may remain within an estuarine region for up to one month, particularly in regions of low water flow. In seasons and regions of relatively high water flows (e.g. the Swan River), accumulations become highly transient, if present at all. At times, and in regions where they may persist, algal accumulations of 5cm or more in depth have an impact on benthic nutrient fluxes. In particular, their presence over sediments of high organic content appears to exacerbate the release of ammonium from the sediment to the overlying water column. Of note, the benthic process Dissimilatory Nitrate Reduction to Ammonium appears to dominate in summer while denitrification rates are minimal, regardless of the presence of a macroagal layer. From these findings, it is recommended that high fluxes of ammonium in the system be recognised In water quality management and nutrient budgets for the system, as It appears that Internal ammonium regeneration Is a large source of Inorganic nitrogen for organisms In the overlying water body, and may support algal blooms In summer. In addition, it appears that the most appropriate method of managing macroalgal distribution and biomass in the system is ensuring strong freshwater flushes during winter periods when macroalgal biomass is largely removed. If seasonal flushes were inhibited, it is predicted that macroalgal biomass and distribution would increase, extending the period that thsy can influence benthic nutrient cycles. The physical removal of macroalgae as a management option in such a scenario would require much time and effort, as the Swan-Canning Estuarine System is such a large system, and macroalgae are spread throughout. Therefore, in modifying river flows into the estuarine system, the quantity, composition and distribution of macroalgae, and possibly other flora and fauna, will be altered. This is already evident in the Canning River, which is regulated and suffers management problems, such as altered species composition, bathymetric changes, toxic algal blooms, and eutrophication.

The use of constructed wetlands and wet detention basins has proven to be highly effective in removing pollutants from industrial discharges and stormwater runoff throughout the world. This is attributed to design of the key treatment components in a constructed wetland, catchment source characteristics and climatic conditions. A disproportionate amount of research and monitoring effort has gone into constructed wetlands due to their cost effectiveness and ability to optimize multiple benefits. In Western Australia, several wetland monitoring studies on the role of constructed wetlands especially in Swan-Canning estuary have been done, but often do not address their design efficiencies in stormwater treatment. Two wetlands (Liege St and Tom Bateman wetland) constructed for nutrient stripping proximal to the Swan-Canning estuary have been monitored for two years. Liege St wetland was constructed to reduce the nutrients reaching the Canning River directly and improve the amenity value of the area. Similarly, Tom Bateman wetland was constructed to reduce nutrients of the Banister Creek catchment draining into the Canning River as well as for stormwater management and habitat use. Physicochemical and biological indicators were used to assess the nutrient stripping efficiency of the wetlands. In some cases, data from previous studies were used to determine the health and viability of the selected wetland sites. The limnological indicators used included; dissolved oxygen, pH, water temperature, electrical conductivity and nutrient levels. The biological included; bacteria, nutrients and chlorophyll in periphyton, macroinvertebrates and diatoms. Differences in the community structure of periphyton, macroinvertebrates and water quality were found from the inlet to the outlet in both Liege St and Tom Bateman wetlands.Despite the poor water quality, Liege St wetland exhibited significant nutrient removal efficiencies for TP while Tom Bateman wetland had very high removal efficiency for TN. The TP removal in Liege St wetland was attributed to the design of key treatment components which included a gross pollutant trap, concrete lined sedimentation pond, vegetated sumplands, weirs and clay lining for the wetland bed. In contrast, Tom Bateman wetland lacked the above key treatment components. Additionally, the wetland experienced short-circuiting especially during high flow periods. The high TN removal in Tom Bateman wetland was attributed to assimilation by plants and micro-organisms especially by the dense growth of Potamogeton crispus observed on the wetland floor and the non- biological transformation processes such as volatilisation, sorption and sedimentation. The poor water quality of the inflow in both wetlands was attributed to catchment characteristics which were not fully investigated in this study. In an attempt to improve the nutrient stripping function of Liege St and Tom Bateman wetland, changes to the wetland design and routine maintenance were suggested for Tom Bateman and Liege St wetland respectively. Also the use of the Swan-Canning Cleanup Programe (SCCP) water quality targets as opposed to the ANZECC trigger values in water quality assessments in constructed wetlands in the Swan-Canning estuary is suggested among others.

The use of constructed wetlands and wet detention basins has proven to be highly effective in removing pollutants from industrial discharges and stormwater runoff throughout the world. This is attributed to design of the key treatment components in a constructed wetland, catchment source characteristics and climatic conditions. A disproportionate amount of research and monitoring effort has gone into constructed wetlands due to their cost effectiveness and ability to optimize multiple benefits. In Western Australia, several wetland monitoring studies on the role of constructed wetlands especially in Swan-Canning estuary have been done, but often do not address their design efficiencies in stormwater treatment. Two wetlands (Liege St and Tom Bateman wetland) constructed for nutrient stripping proximal to the Swan-Canning estuary have been monitored for two years. Liege St wetland was constructed to reduce the nutrients reaching the Canning River directly and improve the amenity value of the area. Similarly, Tom Bateman wetland was constructed to reduce nutrients of the Banister Creek catchment draining into the Canning River as well as for stormwater management and habitat use. Physicochemical and biological indicators were used to assess the nutrient stripping efficiency of the wetlands. In some cases, data from previous studies were used to determine the health and viability of the selected wetland sites. The limnological indicators used included; dissolved oxygen, pH, water temperature, electrical conductivity and nutrient levels. The biological included; bacteria, nutrients and chlorophyll in periphyton, macroinvertebrates and diatoms. Differences in the community structure of periphyton, macroinvertebrates and water quality were found from the inlet to the outlet in both Liege St and Tom Bateman wetlands.
Despite the poor water quality, Liege St wetland exhibited significant nutrient removal efficiencies for TP while Tom Bateman wetland had very high removal efficiency for TN. The TP removal in Liege St wetland was attributed to the design of key treatment components which included a gross pollutant trap, concrete lined sedimentation pond, vegetated sumplands, weirs and clay lining for the wetland bed. In contrast, Tom Bateman wetland lacked the above key treatment components. Additionally, the wetland experienced short-circuiting especially during high flow periods. The high TN removal in Tom Bateman wetland was attributed to assimilation by plants and micro-organisms especially by the dense growth of Potamogeton crispus observed on the wetland floor and the non- biological transformation processes such as volatilisation, sorption and sedimentation. The poor water quality of the inflow in both wetlands was attributed to catchment characteristics which were not fully investigated in this study. In an attempt to improve the nutrient stripping function of Liege St and Tom Bateman wetland, changes to the wetland design and routine maintenance were suggested for Tom Bateman and Liege St wetland respectively. Also the use of the Swan-Canning Cleanup Programe (SCCP) water quality targets as opposed to the ANZECC trigger values in water quality assessments in constructed wetlands in the Swan-Canning estuary is suggested among others.

Non-indigenous species can have significant deleterious impacts on the ecosystems in which they become established. Following the recent establishment of the Striped Sandgoby Acentrogobius pflaumii in the Swan-Canning Estuary, south-western Australia, a study was initiated to determine its spatial and temporal distribution and biological characteristics. Although A. pflaumii was not recorded in the coarse sandy sediment present in the nearshore, shallow waters of the estuary, substantial numbers were recorded on soft muddy sediments in the deeper waters, where it comprised 55% of the total number of gobies. While A. pflaumii dominated the gobiid fauna in Lower Melville Water (~98%), its contributions declined progressively upstream, indicating a preference for waters with a salinity close to that of full strength sea water. Size and age compositions determined that the oldest individual was 3.9 years old and 89 mm in total length, but that the population is dominanted by 1+ individuals. Population mortality and turn-over rates are therefore likely to be very high. Both males and females attained > 87% of their asymptotic lengths (L∞) of 74.9 and 69.3 mm, respectively, during the first year of life, which is characteristic of smaller, shorter-lived species of fish. The results from gonadosomatic indices and the histological examination of gonads suggest that A. pflaumii is able to spawn throughout most of the year, with a peak from November to February. The presence of mature, spawning and depleted gonads in A. pflaumii suggests that this species spawns within the Swan-Canning Estuary. Acentrogobius pflaumii can be thus considered an estuarine & marine species like Favonigobius lateralis. As A. pflaumii attains high densities over a relatively large part of the estuary and can breed within the system, it is likely to be a permanent resident and further work is needed to determine its impact on the native gobiid fauna.

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, among which the Polychaeta, Malacostraca and Bivalvia were the most speciose classes and contributed ~ 38, 23 and 10%, respectively, to the total number of individuals. The total number of species and mean density of macroinvertebrates was far greater at the most protected habitat type (1), which also contained dense beds of seagrass, than at any other habitat type, i.e. 70 species and 209.2 individuals 0.1 m-2, compared to 32 species and 36.9 individuals 0.1 m-2 at the most exposed habitat type (6), which had a substrate comprised only of sand. Differences among habitat type influenced the benthic macroinvertebrate species composition to a greater extent than differences among either zones or seasons. Significantly different faunal compositions were detected among those latter two factors only at the most protected habitat type. The faunal assemblage at habitat type 1 was clearly the most distinct from those at the other five habitat types, particularly in the subtidal zone (R-statistics=0.642-0.831, p=0.1%), and was typified by five abundant polychaete species that were adapted to deposit-feeding. In contrast, the fauna at habitat type 6 was typified by four crustacean species and a species of bivalve and polychaete, whose mobility and tough external surface facilitated their survival and feeding in those turbulent waters. The extents of the differences in species composition among the six habitat types was significantly matched with that among the suite of enduring environmental characteristics that distinguished those habitat types, particularly in the case of the subtidal zone (Rho=0.676). Such results indicated that the environmental variables used to distinguish the nearshore habitat types could be used to reliably predict the types of benthic macroinvertebrate species likely to occur at any site along the lower west coast of Australia. The above biological validation of the nearshore marine habitat classification scheme developed by Valesini et al. (2003) provided the justification for the approach to the second broad aim of this study, namely to develop a quantitative scheme for classifying habitat types in the Swan-Canning Estuary. This approach was similar to that employed by Valesini et al. (2003) in that it considers that differences among habitat types are well reflected by differences in a suite of enduring environmental variables. However, it improves on that earlier method by employing a completely objective and quantitative approach. Thus, a large number of environmentally-diverse nearshore sites (102) were initially selected throughout the Swan-Canning Estuary and a suite of 13 enduring environmental variables quantified at each using remotely-sensed images of the estuary in a Geographic Information System. Such variables were chosen to reflect either (i) the type of substrate and submerged vegetation present, (ii) the extent of exposure to wave action or (iii) the location of the site within the estuary with respect to its vicinity to marine and fresh water sources. These data were then subjected to the CLUSTER routine and associated SIMPROF procedure in the PRIMER v6 multivariate statistical package to quantitatively identify those groups of sites that did not differ significantly in their environmental characteristics, and thus represented habitat types. Eighteen habitat types were identified, which were shown to well reflect spatial differences in a suite of non-enduring water quality and sediment characteristics that were measured in situ at a range of estuarine sites during both summer and winter in 2005 (Rho=0.683 and 0.740, respectively, p=0.1%). However, those latter environmental characteristics required far more time in the field and laboratory to quantify than the enduring variables used to identify the habitat types. Benthic macroinvertebrates were sampled during summer and winter in 2005 in the shallow subtidal regions (~1 m depth) at sites representing eight of the habitat types identified in the Swan-Canning Estuary. These samples contained a total of 51 and 36 species during summer and winter, respectively, and, in both seasons, represented nine phyla, namely Annelida, Crustacea, Mollusca, Sipuncula, Nematoda, Platyhelminthes, Cnidaria, Uniramia and Nemertea. The compositions of the benthic macroinvertebrate assemblages differed significantly among habitat types and, to a similar extent, between seasons (Global R-statistic=0.408 and 0.409, respectively, p=0.1%). However, the spatial differences were considerable greater in winter than in summer (Global R-statistic=0.536 vs 0.280, p=0.1%), presumably due to the greater spatial variation in particular non-enduring in situ environmental characteristics, such as redox depth and salinity. While the number of species, overall density and taxonomic distinctness of benthic macroinvertebrates also differed significantly among habitats, those variables differed to a greater extent between seasons, being greater in winter than in summer. While the measures of taxonomic distinctness tended to be greater at habitat types located in the lower to middle reaches, i.e. habitat types 6, 7, 9, 10, 13 and 18, than the upper reaches i.e. habitat types 1 and 3, the number of species and overall density reflected this trend only during winter. During summer, the mean numbers of species at habitat types 1, 3, 6 and 10 (3.4-6.0) were significantly lower than those at habitat types 7, 13, and 18 (8.8-10.9), whereas the overall density of benthic macroinvertebrates was far greater at habitat type 7 (32260 individuals 0.1 m-2)than at any other habitat type in this season (3135-18552 individuals 0.1 m-2). Overall, the greatest differences in assemblage composition occurred between those at habitat types 1 and 18 (R-statistic=0.669, p=0.1%), which were located in the uppermost region of the estuary and the lower reaches of the basin, respectively, and differed to the greatest extent in their enduring environmental characteristics. The assemblage at habitat type 1, and also that at habitat type 3, located just downstream, were relatively distinct from those at all other habitat types, particularly during winter (R-statistics=0.666-0.993, p=0.1%). The fauna at the first of these habitat types was relatively depauperate, containing low numbers of species and densities, and was characterised by the polychaetes Leitoscoloplos normalis and Ceratonereis aequisetis and the bivalve Arthritica semen. The assemblage at habitat type 3 was also characterised by those three species and the amphipod Paracorophium minor and the polychaete Boccardiella limnicola. In contrast, the assemblage at habitat type 18 was characterised by a more diverse assemblage, i.e. the polychaetes Capitella capitata, C. aequisetis, L. normalis and Pseudopolydora kempi, the amphipods, Grandidierella propodentata and Corophium minor and the bivalve Sanguinolaria biradiata. The number of species was among the highest at this habitat type during both seasons, which was also reflected in the high taxonomic diversity, and the overall density was the highest in winter and second highest in summer. Despite the above faunal differences, those between assemblages at habitat types 7 and 9, which were both located in the basin of the Swan-Canning Estuary, were similar in magnitude to those that occurred between pairs of habitat types located in two different regions of the estuary. Although both habitat types 7 and 9 were characterised by a similar suite of species, i.e. Oligochaete spp., C. aequisetis, C. capitata, C. minor, G. propodentata, L. normalis, and S. biradiata, the substantial differences in assemblage composition between these habitat types in both summer and winter (R-statistics=0.570 and 0.725, respectively) was due to marked differences in the relative contributions of each of these species. Significant and strong correlations were shown to exist in both summer and winter between the pattern of differences in the benthic macroinvertebrate assemblages among habitat types and that among the enduring environmental characteristics used to identify those habitat types (Rho=0.625 and 0.825, respectively, p=0.1%). Furthermore, these correlations were greater than those obtained between the benthic macroinvertebrate fauna and any combination of the non-enduring environmental characteristics (i.e. water quality and sediment parameters) recorded in situ at each habitat type (Rho=0.508 and 0.824, in summer and winter, respectively, p=o.1%). This demonstrates the greater capacity of surrogate enduring environmental characteristics to account for differences in the range of variables that may influence the distribution of benthic invertebrate fauna. Thus, the lists of characteristic benthic macroinvertebrate taxa produced for each of the eight habitat types studied in the Swan-Canning Estuary provide a reliable benchmark by which to gauge any future changes in those fauna. Moreover, these results indicate that the above habitat classification scheme can be used to reliably predict the types of benthic macroinvertebrate fauna that are likely to occur at any nearshore site of interest in this estuarine system. The final component of this study showed that the benthic macroinvertebrate assemblages at four sites in the middle reaches of the Swan-Canning Estuary in 2003/4 differed significantly from those recorded at the same sites in 1986/7. Such differences were reflected in (1) changes in the relative densities of a suite of ten species that were responsible for distinguishing the faunas in these two periods, (2) the absence of 22 rare species in 2003/4 (i.e. 42% of the number of species recorded in 1986/7), (3) the presence of 17 new species in 2003/4, including an abundant polychaete that is likely to have been introduced and (4) a far greater extent of seasonal variation in the number of species and densities of benthic macroinvertebrates in 2003/4. Such changes are likely to be related to lower sediment oxygen levels in certain seasons in 2003/4, as well as an altered hydrological regime due to increased temperatures and decreased rainfall in that more recent period. The fact that these changes have occurred within the Swan-Canning Estuary highlights the need for effective management tools, such as the habitat classification scheme and associated faunal survey undertaken in this study. Such data will provide a sound basis by which to examine the ways in which fauna vary spatially within the system, and allow for the establishment of comprehensive benchmarks for detecting future changes.

Deoxygenation events within the Swan-Canning Estuary are a severe and potentially lethal threat to the resident aquatic fauna and an ongoing concern for management. Hypoxic conditions develop in the upper estuary following heavy rainfall events that deliver an influx of freshwater into the system, stratifying the water column. When tidally driven seawater and freshwater discharge meet, haloclines are formed, creating a barrier to vertical mixing. Organisms living within the stratified bottom waters can rapidly deplete oxygen reserves, eventually causing the lower layers to become hypoxic. The frequency and severity of these events are projected to increase due to climate change as associated reductions in surface runoff reduce river flow (a remediate of hypoxia) and allow deeper penetration of the marine salt wedge, causing prolonged and more intense stratification of the system. In response to this threat, artificial oxygenation plants have been installed in two regions of the upper estuary known to experience hypoxic conditions most frequently in an attempt to maintain dissolved oxygen concentrations appropriate for fauna. Using acoustic telemetry, we tracked fifty-five Acanthopagrus butcheri over a 116-day period between autumn and winter with the aim to relate the patterns of movement (including residency, habitat use and movements on daily and seasonal scales) to a suite of environmental variables commonly associated with the movement of fishes in estuaries, and determine whether the spatial residency of this species is influenced by the operation of the artificial oxygenation plants. The study revealed that detection of A. butcheri was significantly influenced by hypoxia, habitat complexity, salinity and flow, while the operation of the oxygenation plants did not significantly influence A. butcheri detection. Acanthopagrus.butcheri avoided areas wherein large proportions (>20%) of the available habitat was occupied by hypoxia, instead favouring those with <5%. Areas of high habitat complexity owing to the abundance of large woody debris were associated with high numbers of A.butcheri and salinity was a significant predictor of A.butcheri presence with the species being found to favour areas of salinities between 10-20ppt, rarely being detected in waters of <5ppt and >25ppt despite their extreme euryhaline physiology. Thus, the results highlight the species vulnerability to hypoxia and provides further evidence supporting the hypothesis that the habitat compression of A.butcheri is heavily responsible for declines in its condition within the Swan River Estuary. Hence, ongoing management of the Swan-Canning Estuary should aim to mitigate the factors exacerbating hypoxia within the system and incorporate protection and restoration of in-stream woody habitats and riparian vegetation given its importance to native fishes such as A.butcheri as critical refugia. More research will be required to accurately quantify the benefits of artificial oxygenation to estuarine species within the Swan-Canning Estuary.

Aquaculture-based enhancement, a method of releasing cultured organisms into the wild to boost fishery productivity, is becoming increasingly popular as a management option for restoring depleted fish stocks and increasing fishery yields. In the first section of this Thesis, I review and synthesise how the effectiveness of aquaculture-based enhancements can be optimised to maximise survival of released individuals. Two specific areas were identified that have a major influence on the short-term survival of released animals (i) “training” or acclimation in the hatchery to conditions in natural systems, e.g. habitats, water flows, natural (live) food and the smell and sight of predators through predator avoidance training and (ii) the development of a sound release strategy, involving the selection of site, time and size at release. The objective of the second section of this Thesis was to create a tool to inform the development of an optimal release strategy, by evaluating site selection and time of release for the release of post-larval Western School Prawns Metapenaeus dalli in the Swan-Canning Estuary. This was achieved by developing the Survival-Maximisation-At-Release-Tool (SMART), a quantitative tool that collated factors and variables considered to influence the survival of released M. dalli at potential sites around the estuary to determine a SMART score (0-100) for each potential release site and time (Month, Year, Day/Night). Statistical analyses on the resultant SMART scores determined that region of release was the most influential factor for the survival of released M. dalli, followed by year and then month. Due to the wide range of values for the salinity variable and sediment composition and predation factors among sites and time, these had the most influence on overall SMART score. Across the 16 nearshore sites sampled in five consecutive months in each of three years, the optimal site of release was at Deep Water Point in the Lower Canning Estuary during the night in January 2014. Recommendations for future improvements to the SMART methodology for releases of M. dalli were identified and mechanisms for adapting this tool for its application to other species and aquatic ecosystems are discussed. The SMART provides output that can be readily conveyed to diverse audiences (i.e. fishers, researchers, managers and the community) to enhance discussions on optimal release strategies.