Summary 1. Inferring effects of environmental flows is difficult with standard statistical approaches because flow‐delivery programs are characterised by weak experimental design, and monitoring programs often have insufficient replication to detect ecologically significant effects. Bayesian hierarchical approaches may be more suited to the task, as they are more flexible and allow data from multiple non‐replicate sampling units (e.g. rivers) to be combined, increasing inferential strength. 2. We assessed the utility of Bayesian hierarchical models for detecting ecological effects of flow variation by conducting both hierarchical and non‐hierarchical analyses on two environmental endpoints. We analysed effects of discharge on salinity in the Wimmera and Glenelg rivers (Victoria, Australia) using a linear regression with autocorrelation terms, and on Australian smelt in the Thomson River (Victoria, Australia) using a multi‐level covariate model. These analyses test some of the hypotheses upon which environmental flow recommendations have been made for these rivers. 3. Discharge was correlated with reduced salinity at six of 10 sites, but with increased salinity at two others. The results were very similar for hierarchical and non‐hierarchical models. For Australian smelt, the hierarchical model found some evidence that excess summer discharge reduces abundance in all river reaches, but the non‐hierarchical model was able to detect this response in only one reach. 4. The results highlight the power and flexibility of Bayesian analysis. Neither of the models fitted would have been amenable to more widely used statistical approaches, and it is unlikely that we would have detected responses to flow variation in these data had we been using such techniques. Hierarchical models can greatly improve inferential strength in the data‐poor situations that are common in ecological monitoring, and will be able to be used to assess the effectiveness of environmental flow programs and maximise the benefits of large‐scale environmental flow monitoring programs.

Many freshwater fishes are imperilled globally, and there is a need for easily accessible, contemporary ecological knowledge to guide management. This compendium contains knowledge collated from over 600 publications and 27 expert workshops to support the restoration of 9 priority native freshwater fish species, representative of the range of life-history strategies and values in south-eastern Australia’s Murray–Darling Basin. To help prioritise future research investment and restoration actions, ecological knowledge and threats were assessed for each species and life stage. There is considerable new knowledge (80% of publications used were from the past 20 years), but this varied among species and life stages, with most known about adults, then egg, juvenile and larval stages (in that order). The biggest knowledge gaps concerned early life stage requirements, survival, recruitment, growth rates, condition and movements. Key threats include reduced longitudinal and lateral connectivity, altered flows, loss of refugia, reductions in both flowing (lotic) and slackwater riverine habitats, degradation of wetland habitats, alien species interactions and loss of aquatic vegetation. Examples and case studies illustrating the application of this knowledge to underpin effective restoration management are provided. This extensive ecological evidence base for multiple species is presented in a tabular format to assist a range of readers.

We used radio-telemetry to investigate the movement patterns of river blackfish [Gadopsis marmoratus (Richardson)] in Armstrong Creek, south-eastern Australia between August and October 2005. Movements of 11 fish were monitored 2-3 times per week during daylight over 48 days and diel movements of six fish monitored hourly for three consecutive days and nights. Most river blackfish displayed little or no movement during the day and were confined to distinct positions in the stream. However, fish moved over significantly larger ranges and moved amongst mesohabitats at night, which would not have been detected using daylight tracking data only. River blackfish most often were located within pools, but they also commonly used riffle and run habitats. We also found that several fish used inundated riparian areas during a flood and two fish made rapid, large movements coinciding with the elevated flows. This study has revealed previously undocumented aspects of the movements and behaviour of river blackfish. The study has also shown the potential for different conclusions regarding the extent of movement by a species depending on the temporal scale and the timing of observations.

Tributary and mainstem connections represent important links for the movement of fish and other biota throughout river networks. We investigated the timing, frequency and environmental conditions associated with movements by adult golden perch (Macquaria ambigua) between the mainstem of the mid-Murray River and a tributary, the Goulburn River, in south-eastern Australia, using acoustic telemetry over four years (2007–2011). Fish were tagged and released in autumn 2007–2009 in the mid-Murray (n = 42) and lower Goulburn (n = 37) rivers within 3–6 km of the mid-Murray-lower Goulburn junction. 38% of tagged fish undertook mainstem–tributary movements, characterised mostly by temporary occupation followed by return of fish to the original capture river. Approximately 10% of tagged fish exhibited longer-term shifts between the mainstem and tributary. Movement of fish from the tributary into the mainstem occurred primarily during the spawning season and in some years coincided with the presence of golden perch eggs/larvae in drift samples in the mainstem. Many of the tributary-to-mainstem movements occurred during or soon after changes in flow. The movements of fish from the mainstem into the tributary were irregular and did not appear to be associated with spawning. The findings show that golden perch moved freely across the mainstem–tributary interface. This demonstrates the need to consider the spatial, behavioural and demographic interdependencies of aquatic fauna across geographic management units such as rivers.