Coastal marshes serve important ecologic and economic functions, such as providing habitat, absorbing floodwaters and storm surges, and sequestering carbon. Throughout the northern Gulf of Mexico, coastal marshes are disappearing due to wave attack, sea-level rise, sediment export, and subsidence. Marsh area increases when sediments accumulate at the marsh shoreline, accrete vertically, and when non-marsh areas are colonized by marsh vegetation. Marsh shoreline erosion results in net marsh loss when transgression rates at the marsh-water edge exceed upland-marsh migration. The balance between marsh destroying and marsh creating processes determines the long-term survivability of a marsh system. Thus, processes of shoreline change are important considerations when evaluating the overall health and vulnerability of coastal marshes. Shoreline erosion can be measured using remotely sensed data in a geographic information system. Using shoreline position delineated from aerial imagery, historic maps, and field surveys, shoreline change analysis estimates long- and short-term shoreline movements to identify erosion or accretion for coastal marshes at the Grand Bay National Estuarine Research Reserve (GBNERR) and Wildlife Refuge (GBNWR) on the border of Mississippi and Alabama, USA. However, these techniques do not directly provide information on sediment deposition on the marsh surface. To understand sediment deposition, four study sites provide in-situ measurements of sediment deposition using sediment plates and sediment tracers (silica beads) that were collected every three months. Analysis of the shoreline change data and in-situ sediment data for the GBNERR showed that in 2017, all of the shorelines at the study sites are eroding at rates between -0.50 m/yr and -3.39 m/yr, an average rate of -1.45 m/yr. Positive sediment deposition rates were measured from 5-20 meters inland of the marsh shoreline during each season (3-month period) (0.19 ± 0.05 cm [Fall], 0.26 ± 0.11 cm [Winter], 0.48 ± 0.12 cm [Spring], 0.63 ± 0.15 cm [Summer]), indicating sediment deposition increased with every season. Sediment tracer (silica-bead) counts confirmed that sediment was transported onto the marsh surface from eroding marsh shorelines. Higher energy sites had more beads deposited on the sediment plates than the low energy tidal creek site, due to the different wave and tidal conditions between the sites. Increased wave and tidal energy correlated to increased sediment transport further into the marsh. The relative importance of this marsh cannibalism for the long-term marsh survival depends on factors, such as wave attack, as they control the rate of persistent lateral marsh loss. This findings in this thesis suggests that material from eroding marsh edges contributes to the ability of the interior of marshes to maintain their elevation with respect to rising sea levels.

Knowledge of fish habitat use and connectivity is critical for understanding the structure and dynamics of fish populations and, therefore, necessary for the implementation of successful fisheries management strategies. Tagging is an effective means of providing such information, and the elemental composition contained within fish otoliths is increasingly being used as a natural tag. The chemical composition of otoliths reflects the incorporation of elements from different water bodies and can thus be used to understand the habitat use, movements, and life history patterns of fishes. To assess the applicability of otolith elemental composition as a tagging technique within the Tampa Bay estuary, Florida, laser ablation-inductively coupled-plasma mass spectrometry (LA-ICP-MS) was used to analyze the elemental composition of otoliths from two estuarine-dependent fish species, Snook (Centropomus undecimalis) and Red Drum (Sciaenops ocellatus). Otolith elemental fingerprints can be used to quantify the proportion of juveniles from different nurseries that survive to join the sub-adult and adult fisheries, thus, providing resource managers with quantitative criteria to prioritize the most productive areas for conservation and restoration. To evaluate the use of otolith elemental fingerprinting in the Tampa Bay estuary, the spatial and temporal scales of chemical variation in otoliths collected from throughout Tampa Bay were examined by performing permutation-based multivariate analyses of variance (MANOVA) on the elemental data at several spatial (individual tributary, two-region, and three-region) and temporal (annual and seasonal) scales. Canonical Analysis of Principal Coordinates (CAP) was used to generate classifiers based on the otolith elemental fingerprints of juvenile fish, and `leave-one-out' cross-validation procedures indicated that the greatest classification accuracy was obtained by using the two-region model (upper vs. lower Tampa Bay) for both species (for Snook F=45.8, p=0.001, CAP cross-validation success=76%; for Red Drum F=9.7, p=0.001, CAP cross-validation success=87%). For both species, all temporal analyses at the inter-annual scale indicated that otolith elemental fingerprints were significantly different across years (two-way MANOVA; p Several environmental factors which may have contributed to the regional differences in otolith chemistry were examined, including physico-chemical parameters (surface measurements of salinity, dissolved oxygen, pH, and temperature taken at the time of sample collection), surficial geologic stratigraphy, and land development. Weak, but significant correlations were identified between some elements and physico-chemical parameters; however, instantaneous measurements taken at the time of fish collection may not have provided an accurate representation of the overall conditions experienced by the fish during the period in which the otolith material used in analyses had been deposited (2 - 4 weeks). A significant correlation between latitude and otolith Sr/Ca was found, likely corresponding to an increasing ambient gradient that occurs from the upper to lower bay (for Red Drum F=77.1, p=0.001; for Snook F=69.2, p=0.001). The Land Development Intensity metric was negatively correlated with otolith Li/Ca and Sr/Ca. While surficial geologic inputs may have also contributed to the elemental composition of otoliths, the relationships revealed by redundancy analyses (RDA) were somewhat unclear or contradictory. Once the appropriate chemical characterization of the study area was identified (the two-region models for both species), elemental fingerprints from the core portions of sub-adult and adult otoliths were assigned to their most probable juvenile habitat region using a maximum likelihood estimator based on the posterior probabilities generated by CAP analyses (CAP-MLE). Application of the two-region model revealed that the majority of Red Drum (83%) was determined to have originated from juvenile habitats in the upper Tampa Bay region, while most Snook (60%) originated from juvenile habitats in the lower Tampa Bay region. The majority of sub-adult/adult Snook and Red Drum were collected from the same region in which they were determined to have originated (for Snook, 36 out of 55 = 65%; for Red Drum, 58 out of 78 = 74%), indicating some level of site fidelity to juvenile habitat areas. The use of otolith elemental profiling to reconstruct specific environmental and physiological experiences has the potential to provide unique insights regarding the life histories of Snook, a species with unpredictable spawning and movement characteristics. Otoliths from Snook maintained in captivity at the Mote Aquaculture Park (MAP) were analyzed to elucidate the degree to which various factors, including otolith growth (macrostructure features), spawning events, handling stress, and salinity influence otolith chemistry. Cross-correlation analyses of otolith elemental profiles and quantified macrostructure features (including annuli and checks) demonstrated that interpretations of elemental patterns should not be confounded by changes associated with otolith crystallography. An elemental marker for known spawning events was not identified (ANOVA spawners vs. non-spawners, p>0.05); however, because the physiological costs and alterations in blood chemistry associated with gonadal maturation (rather than the singular act of spawning) could affect otolith chemistry, additional studies which more thoroughly track maturation stages may be able to identify a suite of elements that can be used to discern the reproductive histories of Snook. Significantly elevated Zn:Ca (ANOVA: F=5.64, p=0.012) and decreased Fe:Ca (ANOVA: F=25.02, p Continuous life history Ba:Ca and Sr:Ca profiles of 56 wild Snook collected from throughout Tampa Bay revealed significant plasticity in the types of juvenile habitats settled, as well as in the timing of ontogenetic movements from these habitats. Of the profiles examined, 55% exhibited otolith core signatures characterized by an opposing Sr:Ca and Ba:Ca pattern, followed by an inverted pattern, providing an indicator of the movement of larvae from high salinity, pre-settlement environments into mesohaline, tidally-influenced juvenile habitats. In contrast, nearly half (45%) the Sr:Ca and Ba:Ca profiles indicated settlement in higher salinity environments, suggesting a high degree of habitat plasticity for juveniles of this species. For fish that settled into mesohaline habitats, decreases in Ba:Ca and/or increases in Sr:Ca over the first several years of life signaled the ontogenetic transition out of the juvenile habitat, with the timing of emergence ranging from within the first year to age-3. Because conditions during early life may propagate into divergent behaviors in subsequent life stages, information on the experiences of early life and juvenile stages could help to inform whether the occupation of different juvenile habitat types, or the precocious or delayed emergence from those habitats, explain the peculiar spawning and movement habits that occur in this species.

In estuarine and other aquatic systems, it is possible for water to transport locally produced carbon (food) across habitat boundaries, and provide nutrition for animals remote from the carbon source. In estuarine and marine systems, early work examining the movement of carbon from saltmarsh habitats in the USA suggested that carbon may move large distances from inshore to offshore environments. Upon closer examination, however, evidence did not support this paradigm of large-scale carbon movement, referred to as the outwelling hypothesis, in some estuaries. Physical characteristics of estuaries in which large-scale carbon movement did not occur, such as restricted access to the sea, were proposed as a possible explanation, and for these estuaries, movement of carbon among estuarine habitats was considered more likely. A mosaic of saltmarsh and mangrove habitats dominate the subtropical barrier estuary of southern Moreton Bay, Queensland, but there have been no studies that examine the movement of carbon among habitats within this system. Previous studies that examine the movement of carbon have mostly been done in saltmarshes in the northern hemisphere or in tropical mangrove systems. Different vegetation and tidal regimes in temperate marshes of the northern hemisphere preclude generalisations of carbon movement to tropical and subtropical systems. Our understanding of carbon movement in tropical systems may extend to subtropical waters, but the saltmarsh-mangrove mosaic in the subtropics distinguishes them from their tropical counterparts. The mosaic of saltmarsh and mangrove habitats among the barrier islands of southern Moreton Bay thus provide a unique opportunity to examine the small-scale movement of carbon among adjacent habitats in a subtropical system. Stable isotopes of carbon have been used successfully to trace the transfer of carbon from autotrophs to consumers at a range of spatial scales. This method is able to distinguish among carbon sources where autotrophs have different ratios of 13C/12C, and consumers take on the ratio of their food source. The success of stable isotopes in clarifying food web processes, however, depends on isotope ratios changing in predictable ways as elements are processed. As isotope ratios may be influenced by changes in productivity, and differences in nutrient source, they may vary across small and large spatial scales that may confound interpretation of food web processes. In this study I measured small and large-scale spatial variability of three estuarine autotrophs (the saltmarsh grass, Sporobolus virginicus, the seagrass Zostera capricorni and the algal community epiphytic on Z. capricorni) and showed the small-scale spatial variability to be negligible and insufficient to preclude the use of carbon and nitrogen isotopes in food web studies. Large-scale variability was more pronounced and may be useful for spatial correlation of food webs for more mobile species. The small-scale homogeneity and clearly distinguished isotope ratios of the dominant autotrophs in adjacent saltmarsh and mangrove habitats in southeast Queensland are therefore ideally suited to the study of small-scale carbon movement between adjacent habitats. Carbon isotopes of estuarine invertebrates were used to estimate the movement of particulate carbon between adjacent saltmarsh and mangroves at the tens-of-metre scale. Carbon isotope values of two crab species (Parasesarma erythrodactyla and Australoplax tridentata) and two snail species (Salinator solida and Ophicardelus quoyi) in saltmarsh closely match those of the saltmarsh grass, and suggest that the movement and assimilation of carbon occurs at a scale much smaller than has previously been examined. In mangroves, the results of this study indicate that microphytobenthos with some contribution of mangrove carbon is the most likely food source for P. erythrodactyla and A. tridentata, although contribution of carbon from saltmarsh is also possible. Under this latter scenario, carbon movement in mangroves would be considered to occur at a scale larger than that in saltmarsh habitat. A study that examined the movement and assimilation of carbon by crabs and an estuarine slug (Onchidina australis) at a finer resolution (i.e. metres) supported the original findings and indicated that the movement and assimilation of carbon occurs 5 - 8 m either side of the saltmarsh-mangrove interface. At this small-scale, the movement and subsequent foraging of crabs among habitats, the movement of particulate carbon among habitats, or a combination of crab and particulate carbon movement are three alternative models that provide plausible explanations for the pattern in carbon isotope values of crabs. Crab movement among these habitats was measured using an array of pitfall traps perpendicular to the saltmarsh-mangrove interface. To test for carbon movement, samples of detritus were collected at 2 m intervals across this same interface and the carbon isotopes analysed. For the majority of crabs (up to 90% for both species), movement up or down the shore was less than 1 m from the place of initial capture. Thus, crab movement cannot explain the trend in carbon isotope values of crabs. The pattern in detrital isotope values was similar to that of crabs and indicates that the movement of particulate carbon across the saltmarsh-mangrove interface is the most likely explanation for crab isotope ratios. Sources of carbon for estuarine invertebrates can also depend on the size of the saltmarsh patches. Examination of the movement and assimilation of carbon by crabs in saltmarsh patches of different sizes adjacent to mangroves indicates that saltmarshes less than 0.3 ha in area are subsidised by the import of allochthonous carbon, most likely from mangroves. These findings contribute substantially to our understanding of the food web value of estuarine habitats and provide an important link between landscape and food web ecology. They also have important implications for determining the conservation value of estuarine habitats with respect to their functional (food web) value. The scale-dependent sampling used in this thesis also provides important evidence for the fine-scale movement of estuarine carbon that has not previously been examined.

The knowledge and understanding of sediment transport is essential for the development of effective management strategies for nutrient and sediment loading in estuarine systems. Estuarine suspended sediment (in high concentrations), has the ability to adversely impact upon surrounding ecosystems, such as the Great Barrier Reef, Australia. Due to a recent decline in water and sediment quality, it has recently been mandated that a number of tropical, coastal estuarine systems in Queensland, such as the Fitzroy River estuary, have their sediment loading reduced. In order to meet these requirements, a greater understanding of the sediment transport dynamics and driving processes (such as flocculation and settling velocity) needs to be achieved, and the accuracy of estimation improved. This research project was motivated by the need to improve the general accuracy of field measurements for estuarine suspended sediment transport and dynamics. Field-based measurements (especially settling velocity) are necessary for the parameterisation of sediment transport models. The difficulty in obtaining accurate, in situ data is well documented and is generally limited to methods that isolate a water sample from its natural environment, removing all influences of estuarine turbulence. Furthermore, the water samples are often extracted from points (Eulerian) where the history of the suspended particles is generally unknown. These sampling methods typically contain intrinsic errors as suspended sediment transport is essentially Lagrangian (i.e., flows with the net motion of flow-field) in nature. An investigation into different drogue systems conducted in parallel with a study into the tidal states of the Fitzroy River estuary led to the development of a novel Lagrangian drogue device, the LAD. Additionally, the water-tracking ability of the LAD was tested and found to accurately follow a parcel of estuarine water over a slack water period. Therefore the LAD was deployed in the Fitzroy River to assist in the further understanding of complex sediment transport processes such as flocculation and settling velocity in a natural estuarine flow field. The final device (the LAD - Lagrangian Acoustic Drogue) was developed, utilizing the principals of acoustic backscatter intensity-derived SSC measurements. The investigation of a series LAD deployments (during slack water) in the Fitzroy River estuary, revealed the dominant suspended sediment processes and also gave an insight into the prevailing flow-patterns. Results showed the presence of a settling lag mechanism between low and high tide, which can initiate a net sediment flow upstream with each flood tide. The bulk settling velocity showed comparable results at both low and high water. The LAD derived bulk settling velocity as a function of concentration (SSC), yielding a strong positive correlation (r2 = 0.73). Also the importance of flocculation in the bulk settling and clear up of the water column during periods of still water (high and low tide) was demonstrated as all in situ settling velocities (0.33 - 1.75 mm s-1) exceeded single grain approximations (0.47 mm s-1). This research demonstrates the potential for Lagrangian drogue studies as an effective measuring platform for the accurate quantification of estuarine suspended sediment dynamics. The application of the LAD in the Fitzroy River has lead to a significant improvement in the understanding of the system's real sediment transport processes. This research has provided an effective and accurate technique for measuring real settling velocities for input into numerical models or for the validation of existing model outputs. Furthermore, this technique shows great potential for application in other estuarine systems.

Saltmarsh is an important coastal habitat located in the littoral zone of estuaries. Australian saltmarsh area is decreasing due to agricultural and urban development and invasion by mangrove. The aim of the study was to assess the contribution made by saltmarsh as a habitat and a source of food items for fish. Three saltmarsh sites were studied, with Towra Point chosen as a site for detailed ecological study. When corrected for water volume, fish densities were found to be higher within the saltmarsh compared to the adjacent mangrove. Although the fish assemblages in saltmarshes differed significantly from mangroves the overall ratio between commercially and ecologically valuable species in these habitats are similar, a result suggesting the importance of temperate saltmarsh as habitat for economically important fish. Significant export of crab larva from saltmarsh (average crab larval abundance 2124.63 m-3 outgoing water) is a positive contribution to the estuarine food chain supplementing the nutritional requirements of estuarine fish. While the diet of the crabs producing this larvae seems dependant on the saltmarsh environment (given the contrasting isotopic signatures of Sesarma erythrodactyla in saltmarsh and mangrove, and the similarity of isotopic signatures in the saltmarsh for Sesarma erythrodactyla and Helograpsus haswellianus), the crabs do not seem to be dependent on any of the common species of saltmarsh plant, but rather depend on particulate organic matter (POM) derived from local and other sources. Crab larva are a prey item for many estuarine fish, including commercially important species, as evidenced by gut content analysis of fish visiting the saltmarsh flats during spring tides. The results strongly suggest that emphasis be given to ecosystembased management for an estuary rather than component (e.g., vegetation) based managed as defined by the Fisheries Management Act (1994) and the State Environmental Planning Policy 14.

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.

There has been a continuous decline in both the production and general performance of the SRO in NSW estuaries over the past three decades. The relationship of this decline to both environmental and oyster-density related factors are assessed in this thesis. This question has been examined at different scales: a large scale that compares two different estuaries (Clyde and Shoalhaven Rivers, southern NSW); a regional scale that encompasses variations within an estuary and, at a lease scale that examines processes pertaining to individual or small groups of oysters. Levels of inorganic nutrients were in general very low potentially limiting primary production. The limiting nutrient was nitrogen or phosphorus depending on whether long term conditions were dry or wet, respectively. Only during rain events, through the input of terrestrial material, were conditions favourable for fast rates of primary production. Carbon and nitrogen isotope analysis has demonstrated that both external material and local resuspension of the benthos constitute a major proportion of the SRO diet. The uptake of the various food sources also varied considerably depending on local environmental conditions. Increases in SRO growth were strongly correlated to increases in temperature with a low temperature cut-off at ~13°C. Growth also appeared to reduce considerably when salinities lower than ~15ppt persisted for the order of a month. These factors may alter growth through changes in filtration rates. These processes were modelled in a coupled hydrodynamic-NPO (Nitrogen-Phytoplankton-Oyster) model of the Clyde River. This demonstrated that primary production was more affected by estuarine dynamics and nutrient concentrations than oyster uptake. At the current levels of oyster densities, primary production by itself could not account for the observed oyster growth, however growth became realistic with observed levels of POC added to the model. A set of environmental indices were used to complement the model and to assess the sustainability of the culture system. The combined indices indicated that while the ecological carrying capacity of the Clyde was exceeded the production capacity at an estuarine scale was not. On the lease scale, density experiments showed that while growth was not reduced as a result of current stocking densities, the condition index was significantly affected.

Zinc, copper and cadmium accumulation was measured in two herbivorous gastropod molluscs Austrocochlea constricta and Bembicium auratum from Lake Macquarie NSW an area with a history of trace metal pollution. The investigation consisted of three main parts. The first part examined the influence of organism mass and location within the Lake on whole body tissue metal concentrations. This part of the study also compared the distributions of tissue metal concentrations of populations from Lake Macquarie, a known polluted environment, with those of populations from Jervis Bay NSW, an unpolluted environment, to establish whether either species is a net accumulator of zinc copper or cadmium. The second part of the investigation examined a range of factors which may influence whole body metal concentrations. One location in Lake Macquarie was sampled monthly from August 1995 to July 1996. The factors examined were temporal variation, gender, breeding cycle, and tissue distribution. The final part of the investigation examined the detoxification and storage of excess metals in the gastropods from Lake Macquarie. The mechanisms studied were metallothioneins and granules. The tissue metal concentrations of both species were found to be independent of mass. Location within Lake Macquarie did not significantly influence tissue metal concentrations. Variation between individuals was the most significant contribution to overall variation, resulting in a positive skewing of sample trace metal distributions. B. auratum populations from Lake Macquarie had significantly higher copper and cadmium tissue concentrations and A. constricta populations had significantly higher zinc, copper and cadmium tissue concentrations than the populations from Jervis Bay. This suggests that regulation of these metals is not occurring. A. constricta may therefore be considered a net accumulator of zinc, copper and cadmium and B. auratum of copper and cadmium. Tissue metal concentrations did not vary significantly over time. It is suggested that the organisms are in equilibrium with their environment. B. auratum has higher natural equilibrium concentrations than A. constricta particularly for copper and cadmium, suggesting different routes of exposure, uptake or accumulation for the two species. Gender and breeding cycle did not significantly influence tissue metal concentrations. Most of the variability in total copper and cadmium concentrations of both species was explained by variability in gonad tissue metal concentration, while variability in the gonad and somatic tissues zinc concentration explained about an equal amount of the variability in total zinc concentration. A. constricta and B. auratum were both found to induce a cadmium binding protein which has some features in common with metallothionein. A protein of around 10 000 Da which binds approximately 60% of the soluble cadmium was isolated using gel filtration. This protein was further separated into two isoforms using anion exchange. The first isoform eluted at the same time as MT I and the second at the same time as MT II rabbit liver standard. Large cells containing granular material which stained positive for calcium were observed interspersed among the connective tissue immediately behind the columnar epithelial cells lining the gut wall in both species under a light microscope. Calcium positive granular particles were also observed within the columnar epithelial cells of B. auratum. These species have been shown to be net accumulators of the trace metals investigated, with the exception of zinc in B. auratum. It has also been established that organism mass, gender and reproductive state, the partitioning of metals between tissues, and temporal effects are not confounding factors for the purposes of comparing trace metal concentrations between populations. They should therefore be effective biomonitors of the trace metals investigated, with the exception of zinc in B. auratum.

Estuarine ecosystems are under enormous stress due to rapid coastal developments and climate change. Proper management of these important ecosystems requires a good understanding of their key processes. In this thesis, riparian groundwater-surface water interaction is explored for an aquifer-estuary system primarily by a series of numerical experiments. The work focuses on riparian-scale groundwater flow and salinization. The overall aim of the study was to extend our understanding of aquifer-estuary exchange, which is currently centered on the lower marine estuarine reach, to middle estuaries (i.e., the estuary reach that has variable salinity). The numerical experiments were guided by previous studies and observations made from an exploratory field investigation conducted in and next to Sandy Creek, a macro-tidal estuary incised in the alluvial aquifer of the Pioneer Valley, North-eastern Australia (Longitude 49.11°, Latitude -21.27°). The following observations were made from the field investigation: Sandy Creek estuary experiences a variable salinity regime in its mid reaches that consists of periods of 1) freshwater flushing due to up catchment-derived flooding, 2) persistent freshwater conditions for at least 2 months following the flooding, 3) tidal salinity fluctuations and 4) constant near-seawater salinity; laterally extensive and disconnected aquitards were found to occur at the field site; Sandy Creek had an essentially ‘vertical’ bank slope. Numerical simulations were conducted using the finite element modeling code FEFLOW for saturated unsaturated, variable-density groundwater flow and solute transport, to examine the influence of the following factors on aquifer-estuary exchange: a tidally varying estuarine salinity and hydraulic head, a seasonal freshwater flush (i.e., estuary with freshwater and an elevated stage due to an up catchment sourced flood), near estuary aquitard layers, lateral asymmetry (about the estuary centerline) in hydraulic conductivity and regional hydraulic gradients. The simulations neglected seepage face development after numerical experiments showed that for a vertical bank estuary interacting with a sandy loam aquifer, seepage face effects on groundwater flow and associated salinity distribution were minimal. The following observations were drawn from the range of numerical experiments considered. Tidal salinity fluctuations in the estuary (varying between 0 and 1 - i.e., using a relative salinity scale where a salinity of 1 is seawater) produced flow paths and residence times that were distinctly different to the constant seawater salinity case. While the constant average 0.5 salinity case and the corresponding tidally-varying salinity case (i.e., salinity varying between 0 and 1) produced somewhat comparable results in terms of RUC and RLC (RUC represents groundwater discharge to the estuary that originated from recharge to the estuary bank and RLC groundwater discharge to the estuary that originated from recharge through the estuary bed), whereas flow paths and the total salt mass in the aquifer differed. Freshwater flushing simulations indicated that the near-estuary aquifer responds rapidly to a 2-day ‘wet season’ flushing event with a short-lived freshwater lens created through freshening of the hyporheic zone. Annual cycling of the seasonal flushing led to significant disruption of the estuary water circulation in the aquifer thereby impacting on residence times, transport pathways, and RUC and RLC, and acting to potentially remobilize groundwater and contaminants previously trapped in continuous and semi-continuous re-circulation cells. Although groundwater flow paths determined using tide-averaged velocity vectors were representative of flow paths from transient tidally driven flow vector field, residence times calculated from the two flow fields were markedly different. The influence of riparian scale aquitards and lateral asymmetry (about the estuary centreline) in hydraulic gradients and hydraulic conductivity on groundwater flow and associated salinity distribution was also found to be sensitive to estuarine salinity conditions. The results indicate that observations made about aquifer-estuary interaction in the lower estuary may not be directly applicable to the middle estuary. According to the simulations, tidal salinity variations in the estuary are important factors that affect hyporheic-riparian salt transport processes and that the use of a time averaged estuarine salinity as an approximation to variable salinity conditions is unsuitable for the accurate prediction of the near-estuary dynamics in middle estuaries. This study was based on a two dimensional representation of the riparian scale interaction and it is clear that future research needs to focus on the three-dimensionality of the aquifer-estuary system, incorporating spatially and temporally varying flow and transport characteristics. That is, many estuaries are tortuous and the aquifer geology spatially complex such that assumptions required for the two-dimensional section will most likely restrict application to the field. The tidal dynamics in the middle estuary is also expected to generate three dimensional aspects to the aquifer-estuary interaction. Thus further investigation that explicitly models the hydrodynamics and salt transport in the estuary and estuarine morphology is required to refine the insight provided by the simple conceptual model adopted in this study.

The Mark 0. Hatfield Marine Science Center (HMSC) public education opportunities include interpretive programs offered along the Estuary Nature Trail. The purpose of this study was to determine the effectiveness of three informal education programs, interpretive signs, a self-guided trail brochure, and guided naturalist walks, in imparting information on the ecology of estuaries to visitors. A second objective was to determine visitors attitudes towards estuarine and wetland conservation issues. A questionnaire including knowledge and attitude statements and demographics was distributed to 901 participants. Results show that the three programs are effective in teaching visitors about estuarine ecology, with the naturalist walks being the most effective. Knowledge of estuarine ecology and attitudes towards estuarine and wetland conservation issues were associated with visitor characteristics such as level of education, membership in a conservation organization, residence proximity to wetlands, awareness of local wetland controversies, and previous visits to an estuary trail. Observations of visitor behavior along the estuary trail showed that visitor groups spent an average of 16 minutes on the trail. At each interpretive sign between 54 and 77% of the visitors were observed reading the information; those reading times ranged from 16 to 33 seconds per sign. / Graduation date: 1994