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Fish in arid-zone rivers are dependent on waterholes for refuge during drought. In heavily regulated systems, water extraction for human use has the potential to exacerbate drought conditions and increase the reliance of fish on refugia. This study investigated this hypothesis by surveying fish communities at 25 sites in the Ramsar listed Macquarie Marshes, before and after a 23-GL environmental flow event. Although such flows are central to restoration efforts in the Murray-Darling Basin, limited water availability often forces water managers to make difficult triage decisions regarding which ecological assets to service. This study aimed to provide an update on the current health and status of native fish populations in the Macquarie Marshes and discuss how small flows may best be delivered to meet their ecological needs, particularly during droughts. Eight native species were collected, but they were outnumbered by three alien species by more than 3 : 1. Post-flooding recruitment was observed in most species and mean species richness of sampling sites increased significantly, as fish moved out of drought refugia to utilize a more diverse array of microhabitats. This study presents a conceptual model of fish use of refugia and recommends that key low-flow refugia be targeted for remediation efforts. Copyright (c) 2009 John Wiley & Sons, Ltd.