Widespread flooding in south-eastern Australia in 2010 resulted in a hypoxic (low dissolved oxygen, DO) blackwater (high dissolved carbon) event affecting 1800 kilometres of the Murray–Darling Basin. There was concern that prolonged low DO would result in death of aquatic biota. Australian federal and state governments and local stakeholders collaborated to create refuge areas by releasing water with higher DO from irrigation canals via regulating structures (known as ‘irrigation canal escapes’) into rivers in the Edward–Wakool system. To determine if these environmental flows resulted in good environmental outcomes in rivers affected by hypoxic blackwater, we evaluated (1) water chemistry data collected before, during and after the intervention, from river reaches upstream and downstream of the three irrigation canal escapes used to deliver the environmental flows, (2) fish assemblage surveys undertaken before and after the blackwater event, and (3) reports of fish kills from fisheries officers and local citizens. The environmental flows had positive outcomes; mean DO increased by 1–2 mg L−1 for at least 40 km downstream of two escapes, and there were fewer days when DO was below the sub-lethal threshold of 4 mg L−1 and the lethal threshold of 2 mg L−1 at which fish are known to become stressed or die, respectively. There were no fish deaths in reaches receiving environmental flows, whereas fish deaths were reported elsewhere throughout the system. This study demonstrates that adaptive management of environmental flows can occur through collaboration and the timely provision of monitoring results and local knowledge.