Because much ecological research in rivers applies theories developed elsewhere to a diverse array of habitats renowned for their spatial and temporal complexity, riverine ecology lacks a clear conceptual cohesiveness (Fisher 1997). Hence, the quest to identify, explain, and predict dominant ecological patterns and processes has led to the proposition of many conceptual models that also vary across spatial and temporal scales. These models range from the structure of river networks through to reach-scale models of flow regimes, patch dynamics, sediment organization, and stream hydraulics. Not surprisingly, the explicitness of these conceptual models to specific river types (e.g., headwaters, alluvial rivers, floodplain rivers) contributes significantly to the processes and linkages emphasized by the models. Despite the obvious lack of cohesion in conceptual models of river function, three themes are common to all such models and these are fundamental to riverine ecology: (1) identifying interactions between structure and function; (2) understanding the processes driving the arrangement of structural components in space and time; and (3) identifying how specific habitats and processes are connected in space and time. Critical reviews of conceptual models of river function are given elsewhere (see Thorp et al. 2006). Our aim here is to discuss these three themes as they relate to understanding river function.

The deleterious effects of river regulation have been well-documented in rivers worldwide. Although river regulation affects physio-chemical parameters, invertebrate density, richness, community composition and interactions within food webs, these impacts are not always consistent. Restoration of components of natural flow regimes may be beneficial in recovering the ecological integrity of riverine ecosystems. However, the mechanisms are unclear and rigorous testing of the effects of pulsed flow releases has rarely occurred. This thesis aimed firstly to document the effects of river regulation on physio-chemical attributes and invertebrate communities and then test the response to a pulsed flow release. It was hypothesised that regulated rivers would have fewer invertebrate taxa, higher density, altered community composition and increased contribution of autochthonous sources to their diets. A pulsed flow release was hypothesised to decrease the density of invertebrates positively affected by regulation, alter the community composition to more closely resemble that of an unregulated river and increase the contribution of allochthonous sources to their diets. The study was conducted in the upper Hunter Catchment in north-eastern New South Wales, Australia.

Increasing human demand on the world's water resources has led to the construction of dams and diversions that cause major alterations to natural flow regimes and threaten riverine ecosystems globally. Consequently, water resource management now recognises the need to establish the extent to which flow regimes can be altered while maintaining the integrity of the ecosystem. However, the ecological consequences of changing the physical regime are often difficult to predict and, therefore, a well-designed monitoring program, capable of detecting directional change in aquatic biota is critical for assessing human impacts and evaluating the effectiveness of restoration activities. Altered hydrology can affect biofilm assemblages by influencing two counteracting flow-related processes - mass-transfer leading to biomass accrual and shear stress leading to biomass loss. This study uses biofilm assemblages to investigate the biological condition of the regulated Nymboida River, south-eastern Australia, under current flow management practices and to design a monitoring program capable of detecting a change in this condition as flow management practices are altered in the future. The outcome of this study is a scientifically defensible monitoring program that provides meaningful outcomes in both an ecological and managerial context.

This book was written for you if you're interested in the ecology and management of Australia's inland waters, including groundwaters, temporary waters and salt lakes. It is intended to be an introductory text for biologists, water chemists, hydrologists, engineers, consultants, policy makers, social scientists, natural resource managers and the general public - in short, anyone curious about how aquatic ecosystems work and how they are affected by human activities.

Environmental flow rules are developed to provide a flow regime necessary to maintain healthy river and floodplain ecosystems in rivers regulated for human uses. However, few studies have experimentally assessed potential ecological mechanisms causing declines in the health and productivity of freshwater fish assemblages in regulated rivers to inform the development of appropriate environmental flows.We tested whether an experimental flow release in a regulated tributary of the Hunter River, Australia, altered the diet of two widely distributed fish species (Australian smelt 'Retropinna semoni' and Cox's gudgeon 'Gobiomorphus coxii') compared with data from unregulated reference and regulated control tributaries. Neither species had significant differences in the number of prey taxa ingested, gut fullness or composition of gut contents due to the environmental flow release (EFR). The diet of 'R. semoni' did not differ significantly between regulated and unregulated tributaries in either catchment. However, the diet of 'G. coxii' differed in only one of the two pairs of rivers consistently across all sample times. Assuming the EFR was sufficient to alter the composition of prey available for consumption by the fish species studied, our findings imply that functional indicators, such as the diet of generalist higher-order consumers, may be more suitable indicators of long-term flow regime change rather than short-term flow events.

Successful river rehabilitation requires the restoration of self-sustaining ecosystem functions. One key function is organic matter cycling, including the sources, transfers and sinks of organic matter as it moves from the catchment, across floodplains, down streams, and exchanges with groundwater in the hyporheic zone. River food webs may depend heavily on organic matter generated in-stream by microbial and algal biofilms whereas flow pulses may import leaf litter from the floodplain. Bars and riffles retain this organic matter while generating diverse microhabitats whose particular biogeochemical conditions favour different suites of microbes. Poor land management has deprived the Hunter River of geomorphic complexity at the broad scale of bars and riffles. This paper reviews historical changes to channel shape and vegetation regime in the Hunter River and the repercussions of these on organic matter dynamics over the last 200 years. We conclude that introduction of wood will partly restore conditions closer to those pre-European settlement and alter hyporheic processes but that organic matter dynamics may never be fully restored.

Heterotrophic energy pathways play an essential role in the integrity of forested stream ecosystems. In these rivers, leaf-derived energy is assimilated by biota at low trophic levels which is then made available to higher-order consumers by predator-prey interactions. The availability of resources is governed by two key processes; the retention of leaves by physical structures, and the processing of leaves by microbial degradation, and mechanical and biological fragmentation. The reliance on leaves means anthropogenic disturbances such as the clearing of riparian and floodplain vegetation, recolonisation by invasive plants, and changes to in-channel structural complexity can lead to fewer resources for leaf-dependent consumers. Rehabilitation has the potential to restore critical ecosystem functions, although these indicators are seldom included in rehabilitation projects. This thesis examines the potential for rehabilitation with engineered log jams (ELJs) and riparian replantings to rehabilitate detrital energy pathways to degraded coastal rivers.

The natural flow regime of many rivers is threatened by water extraction and other anthropogenic activities. River regulation due to weirs and dams reduces river flows and is associated with declines in habitat condition, decreased water velocity and depth, and loss of wetted habitat. Aquatic invertebrate community structure in different habitats (e.g. slow flowing areas near river margins versus faster flow mid-stream) is largely governed by water depth, velocity, substrate, food availability and physical disturbance through flooding and drying. By studying the distribution of different flow environments in rivers and their benthic invertebrate inhabitants, we may be able to determine which factors are most influential in promoting the maintenance of benthic invertebrate density and diversity, often considered useful measures of 'river health'. This study compared benthic invertebrates in slow and fast flowing habitats between locations upstream and downstream of a weir on the Nymboida River, and along a nearby reference river lacking a weir, the Bellinger River. Survey results indicated that similar densities and diversity of benthic invertebrates occurred on either side of the weir, and that the fauna of the regulated Nymboida River resembled that of the reference Bellinger River. A flow manipulation experiment at two sites upstream and two sites downstream of Nymboida Weir showed that aquatic invertebrate taxa responded within seven days to increases or decreases in velocity. The capacity to respond to flow was not diminished downstream of the Nymboida Weir, indicating that 80 years of river regulation have not had a lasting effect on this aspect of river condition. Flow-dependent (rheophilic) invertebrates may be valuable indicators of an improvement in river condition under enhanced flows.

Community structure and ecological functioning of aquatic ecosystems throughout the world have been impacted by river regulation and intensive land use practices. These modified landscapes provide conditions conducive to the expansion of opportunistic invasive plant species. Although taxa native to south-eastern Australia, 'Typha domingensis' and 'T. orientalis' provide examples of invasive plants becoming an increasing threat to the ecological character of wetlands and creeks of the River Murray, South Australia. Management of these invasives requires frameworks such as adaptive comanagement (ACM) that combine the collaboration of community, stakeholders and scientists with the principle of adaptive management, which is particularly important addressing the management of invasive plants by citizen scientists (wetland managers). This research investigates wetland managers' perceptions of 'Typha'. It also questions whether there is a perceived impact of 'Typha' control on wetland biodiversity as well as their understanding of control methods as part of current wetland management practices. A temporal comparison of remote sensing images revealed that 'Typha' has increased its cover in the Riverland region and is physically blocking waterways and reducing flows, suggesting current control through wetting and drying wetlands and excavation is ineffective. Alternative methods for 'Typha' control were trialled in a field experiment to compare effectiveness and impact on aquatic diversity in both wetland and creek environments. Dredging is the most common control measure in this region and although effective at reducing short-term biomass, causes significant physical damage to habitats. Cutting 'Typha' below water level was also successful in reducing 'Typha' biomass, but the effectiveness of this control measure varied between the wetland and creek site. It is hypothesized that environmental factors intrinsic to each system such as water depth and sediment anoxia potentially limit the effectiveness of control techniques. An important lesson from this research was that some wetland managers' had poor knowledge of Typha and ecosystem responses, information that was key to developing frameworks for effective decisions on Typha control. This emphasises the importance of information exchange among scientists, managers, and communities and learning opportunities through the ACM process to effectively manage invasive native plants in freshwater ecosystems.

Dryland rivers in arid regions of the world support dependant ecosystems under highly variable conditions. The biota of dryland rivers and floodplains has adapted, over time, to the natural cycles of flooding and drying that characterize these environments. Aquatic microinvertebrates form a critical link in the transfer of energy from primary producers to fish and waterbirds that thrive when the rivers rise and floodplains are inundated. Importantly, aquatic microinvertebrates contribute to resiliency of dryland river biota through their ability to form drought-tolerant resting stages during long dry periods. I examined the response of aquatic microinvertebrate communities to changes in environmental conditions, including water regimes, floodplain processes, and habitat availability in the Macquarie Marshes in the arid-zone of western New South Wales, Australia. The Macquarie Marshes are temporary wetlands which have, historically, supported rich and diverse ecological communities such as huge bird colonies of international significance. While these communities have waxed and waned over time with natural flood and drought cycles, anthropogenic changes, in particular modification to the water regime through river regulation and extraction are now altering the normal ecological cycles in the Marshes. ...This study showed that when flooded, the Macquarie Marshes support huge populations of microinvertebrates and correspondingly high numbers of dormant resting stages in dry sediments once the waters have receded. Changes to water regimes that reduce the frequency of flooding and change temporary creeks into semi-permanent water bodies will have a detrimental effect on microinvertebrate communities.