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This study investigated the surface water-groundwater interactions of three semi-and floodplain wetlands of the lower River Murray (SE Australia) using a combination of hydrometric, natural tracer and geophysical methods. The current management objective for these wetlands is to mimic the natural surface water flow regime by engineering wetting and drying cycles for the benefit of the biota. However, the impact this will have on groundwater processes and wetland salinization is unknown. This study found that when inundated, two of the wetlands were groundwater recharge features, whereas the other was a groundwater throughflow system. After these wetlands were dried, there was a reversal of the hydraulic gradients and all three wetlands became groundwater discharge features. The transformation of these wetlands to groundwater discharge features after the removal of surface water means that there is an increased risk of salinization when wetting and drying cycles are reintroduced. In arid/serni-arid regions of the world where wetlands are in direct contact with saline groundwater, extreme caution should be applied when altering the management of the surface hydrology of the wetlands because increases in salinity can impact upon biodiversity. Copyright (C) 2009 John Wiley & Sons, Ltd.