Determining the position of Liman Tepe's (ancient `Clazomenae') archaeological features relative to the coastline is important for understanding their intended function and reconstructing the character of Aegean maritime activities and sea-based trade. Previous attempts at reconstructing harbour locations at Liman Tepe relied on extrapolating paleoenvironments based on modern surface topography. In light of this, samples from a sediment coring survey and terrestrial and underwater archaeological excavations were analysed using multi-proxy geoarchaeological methods to determine paleoenvironmental facies. Micropaleontological (foraminifera), sedimentological (grain-size analysis) and geochemical (δ13C/δ18O) analyses resulted in the reconstruction of the coastal paleogeomorphology, including the presence and absence of ancient harbouring areas. Neither of the previous coastal reconstructions was supported by the new results. Instead, two separate harbouring areas were recognized, one coincident with the Early Bronze Age (4800–3900 years bp) and a second during the archaic and classical periods (c. 2800–2400 years bp). These results emphasize the necessity for multi-proxy geoarchaeological studies when approaching coastal archaeological sites as a means to reconstruct paleocoastal geomorphology and understand ancient maritime development better.