Abstract. The lower reaches of the expansive Murray-Darling Basin, Australia, are a hotspot for freshwater biodiversity. The regional ecosystem, however, has been significantly altered by river regulation, including local and catchment-wide water abstraction. Freshwater fishes have suffered from the resultant altered flow regime, together with other threats including habitat degradation and alien species. Impacts reached a critical point (imminent species extinction) during a prolonged drought (1997)(1998)(1999)(2000)(2001)(2002)(2003)(2004)(2005)(2006)(2007)(2008)(2009)(2010)) that lead to broad-scale habitat loss and drying of refuges during 2007-2010, and urgent conservation measures were subsequently instigated for five threatened small-bodied fish species. A critical response phase included ad hoc interventions that were later incorporated within a broader, coordinated multi-agency program (i.e. the Drought Action Plan and Critical Fish Habitat projects). On-ground actions included local translocation, alien species control, in situ habitat maintenance (e.g. earthworks, environmental water delivery), fish rescues, artificial refuge establishment and captive breeding. Improved river flows signalled an initial phase of recovery in 2011-2012 that included reintroductions. The present paper aims to document the actions undertaken in the Lower Murray, and review successes and lessons from practical examples that will help guide and inform management responses to conserve fish in modified systems subjected to severe water decline.

Most fish recruitment models consider only one or a few drivers in isolation, rarely include species’ traits, and have limited relevance to riverine environments. Despite their diversity, riverine fishes share sufficient characteristics that prediction of recruitment should be possible. Here we synthesize the essential components of fish recruitment hypotheses and the key features of rivers to develop a model that predicts relative recruitment strength, for all fishes, in rivers under all flow conditions. The model proposes that interactions between flow and physical complexity will create locations in rivers, at mesoscales, where energy and nutrients are enriched. The resultant production of small prey will be concentrated and prey and fish larvae located (through dispersal or retention) so that the larvae can feed, grow, and recruit. Our synthesis explains how flow and physical complexity affect fish recruitment and provides a conceptual basis to better conserve and manage riverine fishes globally.

Summary Construction of instream barriers, preventing fish from accessing spawning, nursery and feeding habitat, is a major issue impacting fisheries sustainability throughout the world. Since European settlement, development in the Murray-Darling Basin for irrigation and potable water supplies has led to the construction of over 10,000 barriers to fish movement. The Native Fish Strategy listed fish passage as a major driving action and was proactive in progressing cost-effective solutions to help inform large-scale rehabilitation programmes. The strategy identified a list of high-priority barriers for mitigation works based on feedback from jurisdictional agencies. Research initiatives were then implemented, with measurable outcomes, to help address key knowledge gaps. Research demonstrated that a project to restore passage to the Murray River main channel was meeting all ecological and engineering objectives. Follow-on work identified low-cost mechanisms to improve the effectiveness of existing fishways without compromising ecological functionality. The Native Fish Strategy was also explicit in addressing fish passage issues at irrigation infrastructure and wetland regulators. Work to minimise these impacts included quantifying the scale of irrigation-associated infrastructure and also optimising screen designs to be retrofitted to pump systems to prevent fish entrainment. Options to enhance lateral movement were also identified. The objective of this study is to summarise the fish passage issues progressed by the Native Fish Strategy to develop basin-wide solutions to enhance fish passage over the long term.

Fishways are commonly used to restore native fish movements in regulated rivers. In the Murray-Darling Basin, Australia, 14 fishways are to be built by 2011 to improve passage along 2225 km of the river. The first of these fishways, constructed in 2003, is a vertical-slot design with low water velocities (0.98-1.4 m s −1 ) and turbulence (average 42 W m −3 ). This design was selected to provide passage for individuals between 20 and 1000 mm long. To determine passage success, trapping and a remote automated passive integrated transponder (PIT) tag reading system was used from October 2003 to February 2006. In 57 24-h samples at the exit (upstream end) and entrance (downstream end), 13 species and 30 409 fish were collected at a maximum rate of 4415 fish per day. Fish between 31 and 1030 mm successfully ascended the fishway. However, significantly smaller (<31 mm) fish and small-bodied (<50 mm) carp gudgeons (Hypseleotris spp.), a species previously considered non-migratory, were sampled downstream from the entrance of the fishway. The remote PIT tag reading system revealed that 81% of native golden perch (Macquaria ambigua) and 87% of non-native common carp (Cyprinus carpio) successfully ascended the fishway. These data will help maximise the efficiency of future fishways against a series of pre-determined performance criteria.

Summary Increased regulation and extraction of water from rivers has contributed to the decline of fishes, and the use of environmental water allocations (EWAs) is now a key rehabilitation measure. Major reform of water policy in the Murray‐Darling Basin (MDB), Australia, has recently provided significant EWAs to improve ecological outcomes. Conflict over water buybacks, the value of the water and the need to maximise environmental benefits and minimise risks of unwanted outcomes has increased the expectation for science to underpin and justify such actions. Recent research has focussed attention on the need to understand fish–flow relationships. The Native Fish Strategy for the Murray‐Darling Basin 2003–2013 (NFS), while not specifically targeted at water policy reform or water delivery, has provided fish ecology research and flow restoration experimentation and contributed considerable new scientific knowledge to support flow management. It has contributed to a substantial and positive change in environmental watering for fish, with native fish targets now regularly incorporated into watering objectives. This study documents changes to water management in the MDB, summarises current knowledge of flow‐related fish ecology in the MDB, highlights the benefits and risks of some water management practises and provides recommendations for future management and research. A major recommendation is the need for a coordinated, cross‐jurisdictional approach to flow restoration for native fish, ensuring that the best available science is being used in all watering allocations. We caution on the use of environmental works such as regulators to artificially inundate floodplains and suggest that such approaches should be viewed as large‐scale experiments with the significant risks posed to fish needing to be recognised, adequately monitored and adaptively managed.