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In recent years, there has been a growing interest in the application of geophysical methods to reconstruct the palaeo‐landscapes of sites of special historical interest in support of the planning of archaeological researches. Given the extent of the surface to be investigated, electromagnetic methods have proven to be very suitable for their speed, resolution and versatility for this objective. In particular, coastal areas of the Mediterranean have undergone significant changes in the position of the coastline, because of changes in sea level and sediment inputs that have covered natural harbours used for the establishing colonies. In this paper, we present the results of a geophysical survey conducted using frequency‐domain electromagnetic (FDEM) method carried out to get the geometry of a coastal area near to Emporiae (NE, Spain), which was supposed to form a natural port that was used by Greeks and Romans for its first colonial settlements on the Iberian Peninsula. The results obtained from a dense network of apparent conductivity measurements, supported punctually by other geophysical data (VES and ERT) and boreholes, has allowed us to define the geometry of the basin and confirm the hypotheses of the existence of harbour buried under the coastal and alluvial sediments in the bay close to the remains from Greek and Roman times. [ABSTRACT FROM AUTHOR]