Hypoxic blackwater events occur when large amounts of organic material are leached into a water body (e.g., during floodplain inundation) and rapid metabolism of this carbon depletes oxygen from the water column, often with catastrophic effects on the aquatic environment. River regulation may have increased the frequency and severity of hypoxic blackwater events in lowland river systems, necessitating management intervention to mitigate the impacts of these events on aquatic biota. We examine the effectiveness of a range of mitigation interventions that have been used during large-scale hypoxic blackwater events in the Murray–Darling Basin, Australia and that may be applicable in other environments at risk from hypoxic blackwater. Strategies for hypoxia mitigation include: delivery of dilution flows; enhancement of physical re-aeration rates by increasing surface turbulence; and diversion of blackwater into shallow off-channel storages. We show that the impact of dilution water delivery is determined by relative volumes and water quality and can be predicted using simple models. At the dilution water inflow point, localized oxygenated plumes may also act as refuges. Physical re-aeration strategies generally result in only a small increase in dissolved oxygen but may be beneficial for local refuge protection. Dilution and natural re-aeration processes in large, shallow lake systems can be sufficient to compensate for hypoxic inflows and water processed in off-channel lakes may be able to be returned to the river channel as dilution flows. We provide a set of predictive models (as electronic supplementary material) for estimation of the re-aeration potential of intervention activities and a framework to guide the adaptive.