This paper is an attempt to reconstruct the Holocene geomorphological evolution of the Kambos coastal - alluvial plain, situated in the southern part of the island of Samos between the ancient city of Samos (contemporary city of Pythagorio) and the temple of Hera (Heraion). The present morphology of the site area is shaped by the fluvial action of Mavratza Torrent forming an extensive alluvial fan in the northern part of the plain, while further southwards a drained freshwater marsh close to the sea exists. Heraion is located about 6km westwards of the ancient city. The habitation of the site area started approximately in the 11th century BC and has been constant to this day. Samos city enjoyed its greatest prosperity in the 6th century BC, under the leadership of the tyrant Polycrates. To reconstruct the geomorphological changes of the plain’s area, a detailed geomorphological survey in combination with stratigraphical and palaeontological techniques took place. In addition, a drilling project of two vibracores was carried out. The chronostratigraphy of the cores was determined by two C14-AMS radiocarbon datings undertaken on in situ bivalves. The evaluation of the data gives rise to the following time-scenario concerning the geomorphological evolution of the area. Long before 2700 BC, the area was covered by fluvial sediments originating from the nearby torrents to the north. Predominance of sandy fraction and a low percentage of silty-clayey material may indicate a process that removed the fine material. Absence also of coarse clastics (pebbles, cobbles) indicates restricted fluvial transportation and subsequently a low gradual relief. By ~2700 BC the area had already been flooded by sea-level rise and a shallow lagoon with a sandy bottom was formed. The lagoon continued to exist for a further ~2000 years, progressively becoming muddy; it was restricted and gradually transformed into a marsh. This marsh endured until the final decades of the previous century before it was drained. The aforementioned results strongly encourage the idea that the paved road connecting the ancient city to the temple in the 6th century BC must have been situated more inland, avoiding the coastal lagoon.