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.

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.

Increasingly, interdisciplinary research is acknowledged as essential for resolving problems in conservation (Deem et al. 2001; Stem et al. 2005) and natural resource management (Daily & Ehrlich 1999). Numerous obstacles, however, beset interdisciplinary approaches. Based on her experiences in conservation of sea turtles, Campbell (2005) identifies several of these, including a need to developpublishing protocols, clarify problem definition, integrate assumed objectives, and consider power relations. She suggests that in many conservation research programs, social scientists seem to be "tacked on" to meet funding requirements and typically are invited to join the team after the initial planning stages, severely restricting theiropportunity to contribute to the development of the research program. This, in turn, has implications for the power relations if social scientists are outnumbered by natural science researchers on a team, and she relates that it "is sometimes exhausting to be the one person speaking a different language or trying to represent a broad suite of social-science concerns" (Campbell 2005:576). Her paper concludes by urging researchers to share their experiences with this type of research to provide more knowledge on which potential interdisciplinary researchers might draw. In our interdisciplinary research in ecology, resource management, and education, we also have encountered examples of the obstacles described by Campbell (2005). We agree with many of her recommendations for overcoming these; but rather than tackling these piecemeal, we see a need for a synthetic framework for conducting interdisciplinary research in conservation biology and other research sciences. Our goal here is to introduce and advocate use of an explicit "knowledge structure" to overcomemany of these obstacles.

Urbanisation is acknowledged as one of the most severe threats to stream health, spawning recent research efforts into methods to ameliorate these negative impacts. Attention has focused on streams in densely-populated cities but less populous regional urban centres can be equally prone to some of the same threats yet might not meet the conventional definitions of urban. Several recent reviews have identified the changes to streams that occur during urbanization but they note that few ecological studies have explored eco-system-level responses, typically focusing instead on state variables such as invertebrate abundance. In many regional urban streams, changes to the extent of impervious drainage have implications for their hydrology and channel morphology but the influence of these changes on fundamental ecosystem processes of leaf litter breakdown and transport compared with those in nearby rural streams are poorly known. The widespread practice of planting exotic trees along riparian zones and street margins draining into urban streams further exacerbates the disruption of natural organic matter dynamics. The combination of seasonal leaf fall by exotic species and the altered drainage patterns through urbanization in Armidale, a regional town in New South Wales, Australia, resulted in contrasting patterns of benthic organic matter storage over 18 months compared to nearby reference and rural streams. Macroinvertebrate detritivore densities were low in the urban stream, implying disruption of the usual biological pathways of leaf breakdown. Understanding the interactions of hydrology, drainage pattern, leaf input and biological attribute of a stream is crucial for managers trying to restore stream ecosystem services without incurring public concern about the appearance of regional urban streams.

Defining appropriate environmental flow regimes and criteria for the use of environmental water allocations requires experimental data on the ecological impacts of flow regime change and responses to environmental water allocation. Fish assemblages in one regulated and one unregulated tributary paired in each of two sub-catchments of the Hunter River, coastal New South Wales, Australia, were sampled monthly between August 2006 and June 2007. It was predicted that altered flow regime due to flow regulation would reduce species richness and abundance of native fish, and assemblage composition would differ between paired regulated and unregulated tributaries. Despite significant changes in richness, abundance and assemblage composition through time, differences between regulated and unregulated tributaries were not consistent. In February 2007, an environmental flow release ('artificial flood') of 1400 ML was experimentally released down the regulated tributary of one of the two catchments over 6 days. The flow release resulted in no significant changes in fish species abundances or assemblage composition when compared to nearby unregulated and regulated tributaries. Flow regulation in this region has reduced flow variability and eliminated natural low-flow periods, although large floods occurred at similar frequencies between regulated-unregulated tributaries prior to and during 2006-2007, resulting in only moderate changes to regulated flow regimes. Barriers to dispersal within catchments also compound the effects of flow regulation, and findings from this study indicate that the location of migratory barriers potentially confounded detection of the effects of flow regime change. Further experimental comparisons of fish assemblages in regulated rivers will refine river-specific response thresholds to flow regime change and facilitate the sustainable use of water in coastal rivers.