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In the lower River Murray in Australia, a combination of a reduction in the frequency, duration and magnitude of natural floods, rising saline water tables in floodplains, and excessive evapotranspiration have led to an irrigation-induced groundwater mound forcing the naturally saline groundwater onto the floodplain. It is during the attenuation phase of floods that these large salt accumulations are likely to be mobilised and discharged into the river. This has been highlighted as the most significant risk in the Murray-Darling Basin and the South Australian Government and catchment management authorities have subsequently developed salt interception schemes (SIS). The aim of these schemes is to reduce the hydraulic gradient that drives the regional saline groundwater towards the River Murray. This paper investigates the interactions between a river (River Murray in South Australia) and a saline semi-arid floodplain (Clark’s floodplain) that is significantly influenced by groundwater lowering due to a particular SIS. The results confirm that groundwater extraction maintains a lower water table and a higher amount of fresh river water flux to the saline floodplain aquifer. In terms of salinity, this may lead to less solute stored in the floodplain aquifer. This occurs through three mechanisms, namely extraction of the solute mass from the system, reducing the saline groundwater flux from the highland to the floodplain and changing the floodplain groundwater regime from a losing to a gaining one. It is shown that groundwater extraction is able to remove some of the solute stored in the unsaturated zone and this can mitigate the floodplain salinity risk. A conceptual model of the impact of groundwater extraction on floodplain salinization has been developed.