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The inter-relations between the sea, coastal river and groundwater were studied in the eastern Mediterranean bar-built estuary of Alexander River (Israel), which is subjected to seawater encroachment. In this river, seawater encroachment occurs in response to coastal waves and down-river discharge events. Accordingly, significant stratification occurs mostly during winter (1–3 times a year) following sandbar breaching, with salinities at the deep layer reaching 35 and 27 ‰, 500 and 3,900 m from the shoreline during the study period, respectively. During the summer, the water in the estuary is partially mixed and the salinity in the deep layer significantly decreases, but never below 6 ‰. Salinization of the aquifer adjacent to the river was studied by electrical resistivity and crosschecked with observations in shallow boreholes. Both methods suggest that aquifer salinization is site-dependent, with the extent of salinization being controlled by the local geology. While in sandy units, salinization extends to at least 80 m from the river channel, salinization is limited to no more than 20 m from the river in silty units. The existence of the low-permeability units adjacent to the river prevented salinization of the regional aquifer. Based on these findings, significant salinization impact on the aquifer in the near future due to the ongoing sea-level rise is not anticipated.