Salinisation from rising watertables is a major water resources and land management issue in Australia. Increased irrigation development in the Murray-Darling Basin has led to rising watertables in the adjacent semi-arid floodplains resulting in accelerated salinisation and dieback of riparian vegetation. The ability to model the spatial distribution of salt accumulation has been limited by the lack of an ecologically based framework for representing evapotranspiration from groundwater dependent ecosystems and recharge through episodic flood inundation. A methodology for modelling patterns of groundwater discharge using evapotranspiration theory has been developed and applied to MODFLOW 2000, through the segmented evapotranspiration (ETS) module. Use of this technique has provided insight into the complex relationship between vegetation, soils, elevation and floodplain geometry in groundwater dependent ecosystems, and supported the theory that vegetation type is the primary driver of spatial patterns of groundwater discharge. Geophysical, remote sensing and point scale field measurements such as sap flow were used to validate model outputs. The potential for electromagnetic induction surveys to provide a qualitative means of validating modelled patterns of groundwater discharge and salt accumulation was found to be promising. The study has enabled vegetation health risk resulting from salt accumulation to be identified and aided in appropriate application of management practices such as saline groundwater interception and artificial flood augmentation.