While seawater intrusions are widely discussed, the salinization of coastal aquifers via narrow rivers is hardly documented. This study investigates groundwater dynamics in an aquifer next to an estuarine stream on the eastern Mediterranean coast. Groundwater levels and salinization patterns were examined as a response to dynamic changes in estuary water, both in low-and high-permeability aquifer units. In the high-permeability unit, the extent of salinization was relatively constant, reaching a distance of at least 80 m from the river, with no long-term changes in fresh-saline interface depth, indicating that the system is in a quasi-steady state. Groundwater salinity in the low-permeability unit showed frequent and large fluctuations (up to 36 and 22 at 5 and 20 m from the river, respectively). We suggest that the river may have a more immediate impact on a low-permeability than on a high-permeability aquifer. This is dependent on the history of seawater encroachments to the river, which are better preserved in the low-permeability unit, and on the hydrogeology of this unit, where sand lenses can serve as high-permeability conduits. However, this unit can efficiently prevent a large extent of salinization of the regional coastal aquifer by the estuary water.