The native riparian vegetation communities on the Chowilla floodplain in the lower River Murray in South Australia are suffering severe declines in health, particularly the Eucalyptus camaldulensis Dehnh. (red gum) and Eucalyptus largiflorens F.Muell. (black box) communities. The primary cause of the decline is salinisation of the floodplain soils caused by increased rates of groundwater discharge and hence increased movement of salt up into the plant root zone. The salinity is driven by a lack of flooding and rising saline groundwater tables. Rises in the naturally saline groundwater levels are due to the effects of river regulation from Lock 6 and high inflows from regional groundwater levels increased by Lake Victoria to the east. River regulation has also led to reduced frequency and duration of the floods that leach salt from the plant root zone and supply fresh water for transpiration. The frequency of medium-sized floods occurring on Chowilla has been reduced by a factor of three since locking and water extractions were commenced in the 1920s to provide reliable water for urban and agricultural use. The soil salinisation on the floodplain was modelled by using a spatial and temporal model of salt accumulation from groundwater depth, groundwater salinity, soil type and flooding frequency. The derived soil water availability index (WINDS) is used to infer vegetation health and was calibrated against current extent of vegetation health as assessed from fieldwork and satellite image analysis. The modelling work has shown that there is a severe risk to the floodplain vegetation from current flow regimes. This paper estimates that 65% (5658 ha) of the 8600 ha of floodplain trees are affected by soil salinisation matching a field survey of vegetation health in 2003 (Department of Environment and Heritage 2005a), compared with 40% in 1993 (Taylor et al. 1996). Model results show that the best management option for Chowilla is lowering the groundwater down to 2 m below current levels, which predicts an improvement in the health of the floodplain tree species from 35 to 42%.