Liman Tepe-Clazomenae, located in the southern Bay of Izmir, Turkey, was an important Early Bronze Age to Classical Period trading port and cultural centre in the eastern Aegean. The mainland harbour, now submerged ~1.5–2 m below present sea level, is one of the best-preserved examples of an Iron Age (Archaic Period; ca. 7th–6th c. BCE) semi-enclosed harbour (>5 ha) with engineered breakwater structures. A multi-proxy study (micropalaeontology, micro-XRF core scanning) was conducted on seven harbour sediment cores and integrated with geophysical data to map the harbour structures and document coastal palaeoenvironmental changes. Bathymetry and side-scan mapping revealed two broad (>35 m) rubble-constructed breakwater structures and a submerged headland that divided the harbour into two separate sub-basins. Linear magnetic anomalies within the eastern breakwater indicate a buried pier structure, recording possible augmentation of a Late Bronze Age (LBA) or Early Iron Age (EIA) proto-harbour embayment. The harbour basin stratigraphy comprises foreshore and upper shoreface deposits overlying terrigenous clays across a marine transgressive surface. A distinctive silt-rich chemofacies with increased Ti/Ca and decreased Si marks a transition from a sandy marine shoreface to a low energy, sheltered LBA proto-harbour embayment. The Iron Age harbour construction (ca. 7th–6th c. BCE) is recorded by a rise in Rosalina, decreased Ti/Ca and the appearance of Archaic pottery. The harbour was in use from the Archaic to early Classical periods and served as Clazomenae's mainland commercial port. •Palaeoenvironmental, geochemical and geophysical study of well-preserved Iron Age (ca. 7-6th BCE) harbour•Extensive (>5 ha) harbour facility protected by engineered, rubble-constructed breakwaters•Transition from marine embayment to semi-enclosed harbour recognized in foraminifera, chemofacies•Marine sediment record of Late Bronze-Early Iron Age land use and coastal environmental change