Blackwater events are characterised by a high concentration of dissolved organic carbon in the water column. They occur naturally in lowland rivers with forested floodplains and bring a variety of benefits to both aquatic and floodplain biota. However, particularly when accompanied by high temperatures, respiration of the organic carbon may cause blackwater to become hypoxic. This may lead to a range of lethal and sub-lethal effects on the aquatic biota. We review the current scientific knowledge concerning the management of blackwater and hypoxia, and examine how this knowledge may be applied to the management of hypoxic blackwater events in lowland river systems. A range of management options, which aim to either prevent the development of hypoxic blackwater or to reintroduce oxygen into deoxygenated waters, are reported. Mitigation options that may be applicable to lowland river systems include manipulating the season and magnitude of floods in regulated rivers, increasing rougness in flow paths, establishing oxygenated refugia for aquatic biota and introducing hydraulic structures that promote turbulence and re-aeration. With climatic changes trending towards a scenario where extreme events leading to the development of hypoxic blackwater are more probable, it is now vital to validate and optimise management options on local and regional scales and work towards closing knowledge gaps. With judicious management of regulated rivers, it is possible to minimise the impacts of hypoxic flows while preserving the benefits brought to floodplain and river ecosystems by seasonal flooding and carbon exchange.