Forecast changes in irrigation practices and climate are likely to result in changes to surface and ground water availability for floodplain woodland remnants; however, the potential effects of such changes are poorly understood, with implications for management of woodland remnants for long-term biodiversity persistence. This paper examines Eucalyptus largiflorens floodplain woodland structure and condition in two contrasting regions within the same catchment. It assesses the effects of varying levels of irrigation land use intensity surrounding woodland sites and of flood history within sites, testing the following propositions: (i) floodplain woodlands with greater intensity of surrounding irrigation land use will be in worse condition and have less structural complexity than other floodplain woodlands; (ii) floodplain woodlands with flood histories closer to ‘natural’ regimes will be in better condition and will have greater structural complexity than other floodplain woodlands. This paper demonstrates that where groundwater tables have fallen, rainfall is in deficit and surface flooding occurs less than once every two years, E. largiflorens trees will be in poor condition and are more likely to die. In the absence of sufficient rainfall and groundwater, more frequent flooding is required to maintain E. largiflorens in good condition (less crown death and greater crown density) than would normally be required. Irrigation land use intensity affects variables that create habitat complexity in woodlands, such as the presence of old and young trees, and the abundance of shrubs such as lignum and Sclerolaena. Flow regimes (particularly prior wetting frequency) affect both structure and condition. These results have implications for understanding and management of elements of biodiversity dependent upon the resources provided by floodplain woodlands. They emphasize the importance of maintaining healthy black box remnants in irrigation areas for biodiversity persistence, and suggest that rehabilitation of black box communities in the Lowbidgee using managed flooding could bring significant biodiversity benefits to the region.