Hypoxic blackwater events are characterised by high levels of dissolved organic carbon in the water column,the metabolism of which depletes dissolved oxygen, which can cause fish and crustacean mortality. Understanding the drivers of and controls on hypoxic blackwater events is important in order to reduce the potential for detrimental water quality impacts from both managed and natural flows. After a decadelong drought in south-eastern Australia, a series of spring and summer flood events in 2010-2011 resulted in a large-scale hypoxic blackwater event in the southern Murray-Darling Basin that affected over 2000 km of river channels and persisted for 6 months. We examined the biogeochemistry and hydrology underpinning this extreme event and found that multiple drivers contributed to the development and persistence of hypoxic blackwater. Inundation of both forested and agricultural floodplains that had not been flooded for over a decade mobilised large stores of reactive carbon. Altered flow seasonality, due to a combination of climatic effects and river regulation, not only increased the risk of hypoxic blackwater generation but also shifted the proportion of bioavailable carbon that was returned to the river channels. Hypolimnetic weir discharge also contributed to hypoxia at some sites. These findings highlight the need for a whole-of-system perspective for the management of regulated river systems - especially in the face of a changing climate.