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.

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.

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.

Freshwater ecosystems are under increasing pressure as human populations grow and the need for clean water intensifies. The demand for ecologists and environmental managers who are trained in basic freshwater ecology has never been greater. Students and practitioners new to the field of freshwater ecology and management need a text that provides them with an accessible introduction to the key questions while still providing sufficient background on basic scientific methods. This book represents the only freshwater ecology textbook that is specifically aimed at an introductory level. It will also be a useful primer for students who have not previously taken a specialized freshwater course but who require an accessible overview of the subject.

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).