The analysis of literary sources and historical iconographic documentation, combined with geological data and archaeological records, provides new evidence for the ancient harbour system of Catania. Taking into account the tectonic uplift, during the Greek colonization period the area of Piazza Duomo - the most depressed of the city at the mouth of the Amenano river - was located a few meters below the sea-level. We infer that it was the probable site of a natural inner harbour as a landing place for the first colonists who founded Catania in the 8th century B.C. According to the literary sources, beside the small river port used for commercial purpose, during the Greek and Hellenistic period the large beach located immediately south of the town, now covered by the 1669 lava flow, was used for military purposes. During the Roman period, alluvial episodes and infilling processes led to the final abandonment of the harbour area. Later on, many attempts were made to build a larger and multifunctional harbour, as shown by ancient cartography here considered. From the Roman period to the 19th century, a weak outer mole repeatedly suffered destruction by marine storms from the east. A conclusive role has been played by the 1669 lava flow that not only covered the beach used in the Greek period for military purposes, but also formed a large promontory south of the mouth of the Amenano river, favouring further fluvial-coastal deposition. Finally, the whole area has been absorbed in the town-planning changes related to the modern harbour of Catania.