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.

Approximately 40% of Australian freshwater fish species are of conservation concern, largely because of the impacts of river regulation, habitat fragmentation and alien fishes. Murray hardyhead is a threatened fish endemic to the southern Murray–Darling Basin in Australia, which has declined significantly in range and abundance since European settlement. Conservation of the species has relied largely on environmental watering of off-channel wetlands where isolated populations persist. This became problematic during recent drought (1997–2010) because of competing demands for limited water, and resentment towards environmental watering programs from communities that themselves were subject to reduced water entitlements. In response, emergency conservation measures prioritised the delivery of environmental water to minimise applied volumes. Captive maintenance programs were established for fish rescued from four genetically distinct conservation units, with varying levels of breeding success. Several translocations of wild and captive-bred fish to surrogate refuge sites were also conducted. Future recovery of the species should secure existing natural and stocked populations and translocate fish to additional appropriate sites to spread risk and reinstate natural pathways for dispersal. The approach to the conservation of Murray hardyhead during extreme environmental conditions provides insights to inform the management of fishes in other drought-prone regions of the world.

Summary The Native Fish Strategy (NFS) for Australia's Murray‐Darling Basin was specifically targeted at managing and rehabilitating an entire fish community. Over half of the native fishes (24 of 44 known species) and four fish communities of the Murray‐Darling Basin (MDB) are listed as threatened at either national or state level. One of six ‘Driving Actions’ under the NFS focused on protecting threatened native fish species, and this study reviews a series of NFS case studies during and immediately after the Millennium Drought (1997–2010) which was south‐eastern Australia's worst drought on record. Fish rescues, breeding programmes, the creation of an emergency response contingency fund, and expert panels and workshops were all projects that contributed significantly to conserving threatened fishes. The diversity of approaches taken and lessons learned are highlighted, to formulate future directions for threatened fish recovery.