Native Eucalyptus woodlands on the floodplains of the lower River Murray, Australia are dying because of increased soil salinity associated with shallower watertables and reduced flooding. There is need for a simple salinity index, related to vegetation health, which can be used within a geographic information system (GIS) to evaluate the potential impacts across the floodplain of management options which aim to decrease soil salinity. Management options include increasing the frequency and duration of floods by releasing additional environmental flows from upstream storages or lowering the watertable by groundwater pumping. This paper extends a simple root-zone salt and water balance model which represents the salinisation process as a moving salt front (MSF) [Jolly, I.D., Walker G.R., Thorburn P.J., 1993. J. Hydrol. 150, 589–614; Thorburn, P.J., Walker, G.R., Jolly, I.D., 1995. Plant and Soil 175, 1–11], to develop a flood history weighted net discharge salinity index (WINDS-Index) which relates to vegetation health. The MSF model, based on steady state groundwater discharge theory incorporating water uptake by vegetation, is evaluated against simulations made using a fully dynamic soil-vegetation-atmosphere model (WAVES). These simulations evaluated the impact of groundwater pumping and flooding options [Slavich, P.G., Walker, G.R., Jolly, I.D., Hatton, T.J., Dawes, W.R., 1999. Agric. Water Manage. 39, 241–261]. The dominant features of the WAVES simulations were adequately reproduced using the moving front model, provided the discharge rate was limited to a potential canopy transpiration rate. The WINDS-Index reflects the impact of flooding history on the long term average soil water salinity for soils with varying hydraulic properties, watertable depth and watertable salinity. The WINDS-Index is strongly dependent on the relative inundation time, defined as the ratio of the duration of inundation to the duration between floods, of successive flood events and has application as a management tool within a GIS. The watertable depth for long term control of root-zone salinity is defined using the concept of a critical salt balance criterion which incorporates the relative inundation time and soil hydraulic properties.