This essay briefly reviews perceived values of stygofauna and benefits of their inclusion in hydrogeological surveys of groundwater, and summarises the legislative and policy framework for stygofaunal surveys. Although focused on Australia, the issues discussed are of broad, international concern. A staged approach to surveys is advocated where investigations progressively increase in complexity. This aims to overcome the current paradox of omitting stygofauna from groundwater monitoring because there is insufficient information for the interpretation of survey results — yet, if stygofauna are not sampled, then the information will never be collected to address the knowledge gaps.

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.

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.

Worldwide, the ecological condition of streams and rivers has been impaired by agricultural practices such as broadscale modification of catchments, high nutrient and sediment inputs, loss of riparian vegetation, and altered hydrology. Typical responses include channel incision, excessive sedimentation, declining water quality, and loss of in-stream habitat complexity and biodiversity. We review these impacts, focusing on the potential benefits and limitations of wood reintroduction as a transitional rehabilitation technique in these agricultural landscapes using Australian examples. In streams, wood plays key roles in shaping velocity and sedimentation profiles, forming pools, and strengthening banks. In the simplified channels typical of many agricultural streams, wood provides habitat for fauna, substrate for biofilms, and refuge from predators and flow extremes, and enhances in-stream diversity of fish and macroinvertebrates. Most previous restoration studies involving wood reintroduction have been in forested landscapes, but some results might be extrapolated to agricultural streams. In these studies, wood enhanced diversity of fish and macroinvertebrates, increased storage of organic material and sediment, and improved bed and bank stability. Failure to meet restoration objectives appeared most likely where channel incision was severe and in highly degraded environments. Methods for wood reintroduction have logistical advantages over many other restoration techniques, being relatively low cost and low maintenance. Wood reintroduction is a viable transitional restoration technique for agricultural landscapes likely to rapidly improve stream condition if sources of colonists are viable and water quality is suitable.

1. Water extraction from arid-zone rivers increases the time between floods across their floodplain wetlands. Less frequent flooding in Australian arid-zone rivers has impaired waterbird and fish breeding, killed riparian vegetation and diminished invertebrate and macrophyte communities. Restoration currently focuses on reinstating floods to rejuvenate floodplain wetlands, yet indicators to measure the success of this are poorly developed. 2. We explored the application of criteria for ecologically successful river restoration to potential restoration of floodplain wetlands on the Darling River, arid-zone Australia. Using emergence of micro-invertebrates from resting eggs as an indicator, we compared responses of taxa richness, densities and community composition in floodplain lakes with different inundation histories. 3. Increased drying of floodplain lakes reduced the number of micro-invertebrate taxa. Several key taxa were absent and faunal densities (particularly cladocerans) were reduced when the duration of drying increased from 6 to 20 years. 4. A conceptual model of the ecological mechanisms by which restoration of flooding regime could achieve the target of preserving micro-invertebrate community resilience predicts that reducing the dry period between floods will minimize losses of viable resting eggs. Protection of this 'egg bank' permits a boom in micro-invertebrates after flooding, promoting successful recruitment by native fish and waterbirds. 5. Synthesis and applications. In arid-zone rivers, micro-invertebrate densities and community composition are useful indicators of the impact of reduced flooding as a result of water extraction. Critical to successful native fish recruitment as their first feed and as prey for waterbirds, micro-invertebrates are a potential early indicator of responses by higher trophic levels. Taxon richness, density and key taxa present after flooding, all indicators of resilience, can be incorporated into targets for arid-zone river restoration. For example, one restoration target may be microcrustacean densities between 100 and 1000 L⁻¹ within 2–3 weeks after spring flooding. These criteria can be applied to measure the ecological success of restoration projects seeking to recover natural flood regimes. Given the high economic cost of water in arid zones, convincing demonstrations of the ecological success of environmental water allocations are crucial.

Many rivers are classified as groundwater-dependent ecosystems (GDEs), owing to the contribution of groundwater to their base flow. However, there has been little explicit recognition of the way groundwater influences riverine biota or processes, how degrees of ecological dependency may vary, and the management implications ofthis dependency. The permeable beds and banks of these GDEs where surface water and groundwater exchange are termed 'hyporheic zones'. They are often inhabited by invertebrates, with varying reliance on groundwater, although the ecological roles of these invertebrates are little known. Upwelling hyporheic water can promote surface primaryproductivity, influence sediment microbial activity, and affect organic matter decomposition. In many intermittent streams, variable groundwater inputs alter the duration of flow or water permanence, and the duration and timing of these largely govern the biota and rates of many ecosystem processes (e.g. leaf decomposition). Not only is the physical presence of water important, thermal and chemical conditions arising from groundwater inputs also have direct and indirect effects on riverine biota and rates or types of in-stream processes. Differing degrees of dependency of rivers on groundwater mediate all these influences, and may change over time and in response to human activities.Alteration of groundwater inputs through extraction from riparianwells or changes in localwater table have an impact on these GDEs, and some current management plans aim to restrict groundwater extraction from near permeable river channels. However, these are often ‘blanket’ restrictions and the mechanisms of GDE dependency or timing of groundwater requirements are poorly understood, hampering refinement of this management approach. More effective management of these GDEs into the future can result only from a better understanding of the mechanisms of the dependency, how these vary among river types and what in-stream changes might be predicted from alteration of groundwater inputs.

'Nothing is permanent but change.' --Heraclitus. Research in "pristine" environments provides an intriguing sense of natural river function and evolution (e.g., Collins and Montgomery 2001; Brooks and Brierley 2002). We typically fail to appreciate just how profoundly rivers have been altered by human activities. For example, Brooks et al. (2003) document a 700 percent increase in channel capacity and a 150-fold increase in the rate of lateral channel migration within a few decades of clearance of riparian vegetation and removal of wood from a river in southeastern Australia. Long-term evolutionary insights are required to interpret river responses to human disturbance relative to natural variability. Most rivers have been fundamentally altered from those that existed prior to human disturbance. River systems can be characterized as shifting mosaics of patch dynamic relationships (see chapter 4), for which disturbance is a fundamental requirement for the maintenance of ecosystem integrity. Indeed, change is a natural, vital component of aquatic ecosystem functioning. However, changes to the geomorphic structure of a river can modify and fragment the physical template, severely diminishing its capacity to support ecological systems. For example, substantial declines in the integrity of ecosystems have been associated with habitat change, fragmentation, and loss (Bunn and Arthington 2002; Dudgeon et al. 2006; Postel and Richter 2003).