The development of a standardised means of collecting, analysing and presenting riverine, coastal and estuarine assessments of ecological condition has been identified as a key need for coastal Local Councils who are required to monitor natural resource condition, and water quality and quantity in these systems. Forty-four study sites were selected across the Macleay catchment; 32 freshwater sites and 12 estuarine sites and these were sampled 6 times from April 2015 to February 2016 to contribute to the assessment of the ecological condition of the catchment.

The Macleay River Catchment was divided into four major hydrological units across 22 subcatchments: Tablelands, Macleay River main stem, freshwater tributaries and the estuarine tributaries. The project aimed to:

• Assess the health of coastal catchments using standardised indicators and reporting for estuaries, and freshwater river reaches using hydrology, water quality, riparian vegetation and habitat quality, geomorphic condition and macroinvertebrate assemblages as indicators of aquatic ecosystem health, and
• Contribute scientific information to the development of a report card system for communicating the health of the estuarine and freshwater systems in the Macleay catchment.

Floodplain wetlands are among the most threatened ecosystems in the world. As such, they are frequent targets for management with environmental water with programs aimed at conservation of higher-order, iconic species such as waterbirds or fish. Very few studies have investigated the mechanisms underlying these population level responses, and as a consequence these mechanisms remain poorly understood. There are increasing calls to incorporate trophic dynamics into design and monitoring of environmental flow programs, with a focus on identifying functional rather than population-level responses to management. This thesis aims to use existing and emerging techniques in food web ecology and ecosystem energetics to investigate mechanisms of response to inundation in floodplain wetlands to better inform environmental water management.

Following an extensive review of existing literature, a novel conceptual model of wetland productivity was developed identifying potential links between long and short-term hydrology and trophic dynamics, with specific consideration of resource quality. It proposes that long-term hydrologic maintenance of core wetland habitats will provide detrital-based energy refuges, and that, when hydrologically connected to intermittently inundated habitats that are fuelled by high-quality algal food resources, will substantially improve the trophic carrying capacity of wetlands. The results of a field-based observational study conducted over the course of a managed inundation event partially support this hypothesis.

Hydroperiod is recognised as an important driver of community and food web structure in temporary water bodies. I tested the hypothesis that increased hydroperiod would result in increased food web complexity and food chain length and that these changes would relate to predictable patterns of community assembly related to life history strategies of invertebrate taxa. The study results supported this hypothesis.

I found that the invertebrate community was initially dominated by small-bodied crustaceans and molluscs which likely emerged from desiccation-resistant life stages. This community resulted in a low-complexity food web of short chain length. Immigration and reproduction of largely non-predatory insect taxa in the Filling stage resulted in a mostly lateral expansion of the food web. A subsequent influx of immigrant insect predators in the Drying stage resulted in a significant peak in food chain length and contraction in breadth as the system approached collapse and predation pressure impacted community structure in the lower and intermediate trophic levels.

In addition to investigating the influence of hydroperiod on food web structure, I quantified the total amount of energy produced in the food web at each of three stages of inundation and found a similarly strong influence of increasing hydroperiod on increasing energy production. I investigated energy density on a volumetric basis (i.e. per litre of inundation) and also on a per taxon basis. There was a peak in energy density in the Drying stage as might be expected as a result of habitat contraction. However, energy density was also found to increase over time on a per taxon or functional feeding group (FFG) basis, irrespective of inundation volume. I found a strong correlation between energy density and fatty acid concentration (ρ = 0.669, p = 0.0001), which in turn was related to taxon/FFG occurrence through time. Fatty acid concentration (and therefore energy density) was highest in shredders and predators. The occurrence of these taxa at different stages also had a strong influence on food web structure with shredders and predators contributing to the lateral and vertical expansion of trophic niche space, respectively.

To my knowledge, this is the first study of its kind, tracing energy production and food web structure through time in an Australian wetland and it highlights an interesting area of future research. Understanding the production and transfer of energy, and therefore potential carrying capacity of a system, is vital in setting realistic management goals. Incorporating measures of energy density into food web metrics would provide a valuable additional dimension in understanding trophic dynamics in temporary aquatic systems.

I also modelled predator-prey interactions for aquatic insects using multiple tracers to identify resource use in the lower orders of the aquatic food web, and sought links to hydrology. To do this, I employed a relatively new method incorporating stable isotopes of δ13C, δ15N and selected fatty acids in the Bayesian mixing model MixSIAR. A significant challenge in employing this method is the lack of robust calibration co-efficients (or trophic discrimination factors [TDF]) for fatty acid metabolism for many taxa. I identified a set of TDFs that performed reasonably well when considered against known diets. However, this study served to highlight the need for more experimental work to develop robust data for model parameterisation.

Overall, this project identified several interesting areas for further research including incorporation of energy density measures into food web studies, identifying links between trophic level and energy density, and experimental feeding trials to identify energy transformation pathways in aquatic insect taxa. Several important links to hydrology were revealed and the results offer some potentially valuable considerations for water management in floodplain wetlands.

The development of a standardised means of collecting, analysing and presenting riverine, coastal and estuarine assessments of ecological condition has been identified as a key need for coastal Local Councils who are required to monitor natural resource condition, and water quality and quantity in these systems. Thirty-one study sites were selected across the Nambucca River and Deep Creek catchments; 18 freshwater sites and 13 estuarine sites and these were sampled 6 times from July 2016 to June 2017 to contribute to the assessment of the ecological condition of the catchment.

The Nambucca Ecohealth program was divided into six major hydrological units across nine subcatchments: Nambucca River (North Arm), tributaries of the Nambucca North Arm, Taylors Arm, tributaries of Taylors Arm, and Warrell Creek in the Nambucca catchment; and Deep Creek, an ICOLL (Intermittently Closed and Open Lake or Lagoon) to the north of the Nambucca catchment. The project aimed to:

• Assess the health of coastal catchments using standardised indicators and reporting for estuaries, and freshwater river reaches using hydrology, water quality, riparian vegetation and habitat quality, geomorphic condition and macroinvertebrate assemblages as indicators of aquatic ecosystem health, and
• Contribute scientific information to the development of a report card system for communicating the health of the estuarine and freshwater systems in the Nambucca River and Deep Creek catchments.

Floodplain wetlands play a significant role in the storage of sediment and water and support high levels of nutrient cycling driven by intermittent inundation. In regulated rivers, the frequency and duration of floodplain inundation are often reduced. Managed water inundation is used as a tool to help restore floodplains, but its outcome on wetlands requires further quantification. We examined the effects of environmental floodplain watering on water quality and 3 groups of invertebrates, including benthic and pelagic micro invertebrates and macroinvertebrates, in 2 wetlands systems on the Gwydir River system in the north of the Murray-Darling Basin. We hypothesised that a wetland inundated for longer periods would alter water quality and support a greater richness and abundance of invertebrates, thus altering their assemblage structures. Water quality and the assemblage structure of all 3 invertebrate groups in the wetlands were significantly influenced by the time since connection (TSC) to their rivers and therefore the length of inundation. However, the response of water quality and the micro invertebrate assemblages to TSC differed between the 2 wetlands. Water quality was affected by an increase in 6 variables, including total nitrogen, and a decrease in soluble reactive phosphorus. Micro invertebrate abundance was positively associated with TSC, but the abundance of macroinvertebrates was not. The relationships demonstrated between TSC and invertebrates indicate that the duration of inundation is important for ecological structure and food webs in these and other semiarid floodplain wetlands.

Wetlands, which are considered as one of the most critical and valuable ecosystems on Earth, provide a wide range of critical ecosystem services to ecology and the human community. The Mekong Delta (MD) in Vietnam, a huge tropical wetland, is dominated by three key wetland types: mangroves in coastal zones, inland and coastal Melaleuca wetlands and important human-made wetlands (i.e., paddy ecosystems). The wetlands in the MD significantly contribute to ecosystem services and livelihoods of local communities. For example, forest wetlands regulate water balance, provide forest commodities, and conserve biodiversity. Meanwhile, paddy fields play important roles in food security and ecosystem protection and conservation. Moreover, the wetlands greatly contribute to socio-economic development and alleviation of poverty and hunger by offering resources, including food, medicine, other non-timber products, and eco-tourism resources.

However, the wetland ecosystems are under threat from regional anthropogenic, global climate change, and the associated sea level rise (SLR). Particularly, the coastal wetlands (mangroves and coastal Melaleuca wetlands) are susceptible under SLR and changes in local climates including altered water balance, higher temperatures, and extreme events such as floods and droughts. For the case of paddy ecosystems, climate change with greater intensity and frequency of floods and droughts in combination with salinity intrusion due to SLR in recent years have already challenged rice crop production in the MD, subsequently threatening food security.

Understanding the long-term changes in wetlands and exploring their driving factors are important for protecting and conserving wetland ecosystems and their critical services. Additionally, identifying potential impacts of changes in climate variables and SLR on wetlands is fundamental for the development of management, mitigation and adaptation strategies, which can be used to minimize the impacts of climate change and to protect and conserve the wetlands. Even though several studies have been undertaken concerning wetland ecosystems in the MD, the dynamics and drivers of these important wetland areas, and the potential impacts of changes in climate and SLR on the important wetlands are not yet well documented or researched. Therefore, this study aimed to investigate the long-term changes to wetlands under climate and environment impacts and to project future climate change and its impact on wetland ecosystems in the MD, Vietnam using remote sensing, GIS, ecological niche models, and climate models.

The wetland ecosystems in the south-west coast of the MD have experienced critical changes over the period 1995/2020. The substantial increase in aquaculture ponds is at the expense of mangroves, forested wetlands, and rice fields, while shoreline erosion significantly affected coastal lands, especially mangrove forests. The interaction of a set of environmental and socio-economic factors were responsible for the dynamics. In particular, SLR was identified as one of the main underlying drivers" however, the rapid changes were directly driven by policies on land-use for economic development in the region. The trends of wetland changes and SLR implicate their significant effects on environment, natural resources, food security, and likelihood of communities in the region sustaining for the long-term.

The study used GIS-based fire danger modelling approach and remote sensing techniques to evaluate the fire danger and its potential impacts on land-cover and wetlands in the MD. The change in climate with prolonged drought and high temperature is likely to cause serious fire danger. Importantly, forests, especially Melaleuca forests in U Minh wetlands, and agricultural land were under severe fire danger. Hence, measures such as proper management of forests and agricultural activities for mitigating forest fires and integrated fire and water strategies for either fire danger mitigation or biodiversity conservation are necessary for sustainable management of the MD wetland.

This study also examined the potential impacts of climate change and SLR on the three dominant species of these wetland types, Avicennia alba (A. alba) and Rhizophora apiculata (R. apiculata) in mangrove wetlands and Melaleuca cajuputi (M. cajuputi) in Melaleuca wetlands, utilizing an species distribution model (SDM) approach. The projected reduction in habitat suitability of A. alba, R. apiculata, and M. cajuputi by mean values of 27.9%, 28.7% and 30.0%, respectively by the year 2070 indicates the vulnerability of the wetland species to climate change impacts. Increases in temperature, and in seasonal variation in precipitation and temperature, and SLR were key driving factors responsible for the losses of suitable habitat.

Potential changes in mangrove distribution in response to future SLR scenarios in the coastal area in the south of the MD were investigated using the Sea Level Affecting Marshes Model (SLAMM). Simulation results show that the average annual mangrove losses are likely to be 0.54% and 0.22% for subsidence and stable scenarios, respectively. The findings demonstrate the considerable impacts of SLR on MD mangrove ecosystems, and the strong influence of subsidence processes. The findings from the present study are useful sources for development of proper strategies for minimizing the impacts of SLR on mangrove ecosystems and their vital associated-services, to protect and conserve the mangrove ecosystems in the region.

The current work also identified changes in habitat suitability for a coastal Melaleuca wetland species in response to different future climate change and SLR scenarios, in the West Sea of the MD, with the aid of an ensemble SDM and the SLAMM. Simulated results suggested mean losses in suitable habitat of 29.8% and 58.7% for stable and subsidence scenarios, respectively, for the year 2070 in comparison to the baseline scenario. Relative SLR with considerable subsidence rate was suggested as one of the main drivers responsible for the habitat suitability loss.

The use of ensemble SDM approach to examine the potential impacts of climate change and SLR on paddy ecosystems also demonstrates the vulnerability of the ecosystems under future climate and SLR scenarios. In particular, the mean loss of suitable land and mean gain of unsuitable land were 31.4% and 64.6%, respectively, for the year 2050 compared to the present. Salinity intrusion, increases in precipitation during rainy season and decreases in precipitation during dry season were key factors driving the loss of suitable habitat. The findings of this study critically support policy makers and planners in developing appropriate strategies for adaptation and mitigation in response to climate change for sustainable rice cultivation.

Generally, the obtained findings provide valuable information on how climate and environment variability affect wetland ecosystems. Moreover, the outcomes of this study will provide statistical and spatial data on the current and future changes of wetland habitat suitability in the MD. The valuable knowledge and critical data will support the government, planners, policy makers and private investors in developing appropriate management, adaptation and mitigation strategies for protection and conservation of the wetland ecosystems in the region under future climate.

The Basin-wide Environmental Watering Strategy forms a part of a program of water reform in the Murray-Darling Basin to deliver water to instream channels and wetlands through environmental flows. A key objective of the Strategy is 'Improved Ecological Processes' based on more productive and diverse food webs and ecological communities supported by the increased movement of carbon and nutrients. In turn, achieving these productivity and water quality objectives supports the Basin Plan Objectives of improving the life cycle completion of key plants and animals, and meeting the needs of the whole fish and waterbird community. Therefore, key Basin Environmental Watering Strategy targets of successful fish and waterbird recruitment can only be achieved if environmental water delivers sufficient energy that is both available to, and accessible by aquatic biota.

In this report we assess the responses of three groups of aquatic invertebrates, including epi-benthic and zooplankton microinvertebrates and macroinvertebrates to the environmental water releases and natural flows that occurred in the channels in Gwydir River Selected Area during the Long term Intervention Monitoring (LTIM) program. We found that the responses in either richness or abundances of individual taxa due to various associations with channel hydrology significantly affected in assemblage structure of all three invertebrate groups. The response of invertebrates to channel hydrology was mainly demonstrated for epibenthic and zooplankton microinvertebrates and not macroinvertebrates but those associations were not strong. Due to the presence of invertebrates at all sites and times when water was available environmental water can play a significant role in contributing to the basal food resources in the Gwydir Selected Area.