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The transport of saline groundwater from local and regional aquifers to the lower River Murray in South Australia is thought to be greatly influenced by the incised lagoons and wetlands that are present in the adjacent floodplain. Interactions between a saline lagoon and semi-confined aquifer at a floodplain on the River Murray were studied over a 1-year period using hydrogeological techniques and environmental tracers (Cl(-), delta(2)H and delta(18)O). Piezometric surface monitoring showed that the lagoon acted as a flow-through system intercepting local and regional groundwater flow. A chloride mass balance determined that approximately 70% of the lagoon winter volume was lost by evaporation. A stable isotope mass balance estimated leakage from the lagoon to the underlying aquifer. Around 0-38% of the total groundwater inflow into the lagoon was lost to leakage compared to 62-100% of groundwater inflow lost to evaporation. Overall, floodplain wetlands of the type studied here behave as groundwater flow-through systems. They intercept groundwater discharge, concentrate it and eventually recharge more saline water to the floodplain aquifer. Understanding groundwater-surface water interactions in floodplain wetlands will benefit the effective management of salinity in semi-arid rivers. Copyright (C) 2009 John Wiley & Sons, Ltd.