This paper investigates the complex interaction between a river and a saline floodplain in a semi-arid environment strongly influenced by groundwater lowering using a fully integrated physically-based numerical model. The main objective is to quantify the impacts of river stage manipulation on freshening of the shallow floodplain groundwater through bank storage. It is shown that river stage rises produce a relatively less saline floodplain aquifer with a larger freshwater lens. First, an increase in river stage reduces saline groundwater recharge to the floodplain. Second, the enhanced bank storage is able to freshen the groundwater near the river banks during high-flow pulses by mixing fresh water with saline groundwater. Overall, it was found that river stage manipulation may be considered as a short term salt management technique. However, if longer term strategies are required, it may be possible to implement these salt interception measures periodically.