An on‐land frequency domain electromagnetic geophysical survey was conducted across a tombolo delimiting the southern bay of Tel Dor (northern Israel) to the south. It was accompanied by a marine archaeological survey adjacent to its northern edge. Results indicate a deep channel connecting the bay and the Tantura Lagoon to the south. At its northern exit, an NW–SE trending square anomaly is visible in the geophysical data, buried underneath centuries of sand accumulation. It is parallel and similar in shape and scale to a Hellenistic feature observed in satellite data and excavated during the underwater archaeological survey. It seems that during the beginning/Middle Bronze Age, a natural or manmade channel was utilized as an entrance to the bay. As sea levels rose and sand began to accumulate, the channel was periodically filled in and would have needed to have been cleared. Eventually, it became too expensive or inconvenient to maintain, probably during the Byzantine period. The southern anchorage was abandoned for more favorable conditions to the north of the Tel. The sequence of events shows how ancient builders first utilized a natural channel, maintained it as sea levels rose, and abandoned it when it became too problematic to maintain.