AbstractThis study presents the groundwater flow and salinity dynamics along a river estuary, the Werribee River in Victoria, Australia, at local and regional scales. Along a single reach, salinity across a transverse section of the channel (~80 m long) with a point bar was monitored using time‐lapse electrical resistivity (ER) through a tidal cycle. Groundwater fluxes were concurrently estimated by monitoring groundwater levels and temperature profiles. Regional porewater salinity distribution was mapped using 6‐km long longitudinal ER surveys during summer and winter. The time‐lapse ER across the channel revealed a static electrically resistive zone on the side of the channel with a pronounced cut bank. Upward groundwater flux and steep vertical temperature gradients with colder temperatures deeper within the sediment suggested a stable zone of fresh groundwater discharge along this cut bank area. Generally, less resistive zones were observed at the shallow portion of the inner meander bank and at the channel center. Subsurface temperatures close to surface water values, vertical head gradients indicating both upward and downward groundwater flux, and higher porewater salinity closer to that of estuary water suggest strong hyporheic circulation in these zones. The longitudinal surveys revealed higher ER values along deep and sinuous segments and low ER values in shallow and straighter reaches in both summer and winter; these patterns are consistent with the local channel‐scale observations. This study highlights the interacting effects of channel morphology, broad groundwater–surface water interaction, and hyporheic exchange on porewater salinity dynamics underneath and adjacent to a river estuary.