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.

In 2005, I outlined what I considered to be some of the chances and challenges in the conservation of groundwaters and their dependent ecosystems (Boulton, 2005). My goal was to highlight the conservation significance of the hydrological linkages of surface waters and associated systems (e.g. riparian zones) to groundwaters and how we might protect such 'open' aquatic ecosystems. I briefly reviewed what we knew then about the ecology of groundwaters and ground-water dependent ecosystems (GDEs), explored some of the threats disrupting flows of water and energy to these systems, and concluded by identifying chances and challenges in their conservation. I said then — and I still believe — that our biggest challenge as aquatic conservationists is to increase (and sustain) public and political awareness of the importance of groundwaters and GDEs, how they are threatened, and the need for applied research on groundwater processes and response functions to help managers assess groundwater resource use. My pleas echoed those of others (e.g. Humphreys, 2000; Danielopol et al., 2003); now it is time to take stock of their effectiveness. What have we learned in the last half-decade? How successfully are we using this information to protect and conserve global groundwaters and their dependent ecosystems?

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.

Although we are still developing our understanding, there is increasing recognition that groundwater is essential to many ecological communities. Groundwater is a connector, not just in the aquifer itself, but within, across, and between surface waters and many terrestrial ecosystems. Where the water table intersects or comes close to the land surface, contributions of water and nutrients to plant roots and aquatic ecosystems can be critical to their persistence. Consider that precipitation is the dominant source of water in nearly all wetland systems, yet the influence of the lesser groundwater flow component can be sufficient from an ecological perspective to yield an entire new type of wetland, the fen. Influxes of groundwater to lakes, rivers, and wetlands can change whole-system physico–chemical properties such as temperature and salinity, while also providing more subtle influences on microenvironments and their ecological processes. Infiltration of water from surface aquatic ecosystems and rainfall can have an equally significant effect on aquifer ecology, especially on microbes and subsurface invertebrates. Whether water is flowing into or out of an aquifer, or is moving from one part to another, it is the extent and intensity of connectivity that often determines its importance to ecosystems. Moreover, the same location in space can have all three types of flows at different periods of time. Surface ecological processes (such as evapotranspiration) can significantly impact hydrological responses and related hydrochemical function. Thus, the relation of groundwater hydrology to patterns and processes in ecology is a 'two-way street' where understanding the feedback of one to the other serves as a powerful lens through which to evaluate and explain the functioning of natural ecosystems.

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.