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Saline irrigation drainage water along the semi-arid lower River Murray is often disposed of into evaporation basins to prevent contamination of downstream water supplies. These evaporation basins are often former ephemeral floodplain wetlands that have now become extremely ecologically degraded due to high soil and water salinity. An experimental flooding with freshwater was conducted at Loveday Disposal Basin in 2006 to evaluate the environmental benefits of periodic flooding with freshwater. The water and salt balances of the permanent North Basin and ephemeral South Basin during the experiment were evaluated using a combination of hydrometric techniques and trends for salinity and the stable isotopes of water. Filling of the basins (with freshwater from the River Murray) decreased salinity (as total dissolved solids) from approximately 60 to 9 g I(-1). Once flooding was completed, water level in both basins receded rapidly and then within 5 months they had re-salinised to pre-treatment levels. The main re-salinisation mechanism was greater evaporative loss induced by the large increase in wetted surface area after flooding, especially in the shallower South Basin. Dissolution of evaporites was not a source of salt to the basins because halite remained undersaturated at all times, but minor quantities of Ca(2+) and SO(4)(2-) were gained from gypsum and carbonate dissolution. The salt mass stored in South Basin surface water increased during flooding and early after flooding, suggesting a significant salt input from the flooded soils. Because of large salt stores in surrounding soils and groundwater, ongoing saline groundwater discharge, and large evaporative losses, periodic flooding alone brings limited environmental benefits (that is, conditions favourable to freshwater organisms) to floodplain disposal basins. However, flooding deeper disposal basins during winter will minimise evaporative losses and increase the length of the freshening period. Copyright (C) 2009 John Wiley & Sons, Ltd.