Ancient harbour sediment archives can provide long-term records of changes in coastal palaeoenvironments, settlement history, and anthropogenic impacts on coastal systems. In this study, multi-proxy geoarchaeological investigations were conducted at two long-occupied coastal archaeological sites (Liman Tepe-Clazomenae, western Anatolia, Turkey; Lechaion, northeast Peloponnese, Greece) to document coastal palaeoenvironmental change and harbour basin evolution. Multi-proxy core analyses (micropalaeontology, sedimentary facies) were integrated with geophysical mapping and micro-XRF core scanning (chemofacies) to investigate harbour sediment archives and to reconstruct coastal palaeoenvironments. At Liman Tepe-Clazomenae, the Neolithic to Early Bronze Age (ca. 6700-3000 BCE) coastal palaeogeography was reconstructed using a large subsurface database (>20 cores, ~600-line km geophysical surveys) to determine palaeoshoreline positions and potential locations of prehistoric proto-harbour basins. Geophysical mapping revealed a submerged palaeolandscape with relict river channels and shorelines recording inundation of a middle Neolithic coastal plain. A transgressive systems tract was identified by marine foreshore and shoreface deposits overlying paleosol and lagoonal sediments. Shoreline positions were estimated by back-strip analysis of the de-compacted sediment thickness from the marine transgressive surface. During the middle Neolithic (ca. 6700 BCE) the shoreline was >500 m seaward of the modern shore and transgressed to its maximum extent (~1 km inland) during the Chalcolithic (ca. 4000 BCE). After 4000 BCE, sea level decelerated and the coastline prograded under a high-stand systems tract by barrier accretion. The transition from a Late Bronze Age (LBA) proto-harbour to Iron Age semi-enclosed harbour basin was recorded by shifts in geochemical proxies (Ti/Ca, Si, Br), foraminifera, and sedimentary facies. Shifts in Ti/Ca record potential signals of land clearance and evidence for a 300-year LBA drought period (“Greek Dark Age”). Geophysical mapping of Clazomenae’s Archaic (ca. 7th-6th c. BCE) harbour basin revealed two rubble-constructed breakwater structures and a submerged headland separating east and west basins. Linear magnetic anomalies within the eastern mole indicate a buried (LBA?) pier or breakwater within the rubble mass. At Lechaion, a multi-proxy analysis was conducted on seven cores to determine the timing and causes of the Roman harbour decline and abandonment. Coring identified a basin-wide paraconformity surface separating harbour sediments and overlying marl deposits, which records a rapid transition from a marine-estuarine to restricted evaporitic lake environment. Rapid basin restriction was indicated by a decrease in terrigenous elements (Si, Ti, K, Fe), increased Sr and δ18O, and a shift from marine-estuarine to marsh-freshwater taxa. The event records the 6th c. CE tectonic uplift and destruction of the harbour basin, linked with uplift on the nearby Perachora Peninsula (~1.1 m) during destructive earthquakes in 524 and 551/552 CE. No evidence was found for tsunami events proposed in previous work. This study has documented the development, evolution, and abandonment of harbour basins on two tectonically active coastlines with complex relative sea level histories. Palaeogeographic mapping at Liman Tepe has identified a drowned palaeolandscape with areas of high archaeological potential for submerged prehistoric sites and proto-harbour anchorage areas. At Lechaion, multi-proxy analysis has resolved a long-standing debate, demonstrating that the harbour basin decline in the 6th c. CE was caused by coastal tectonic uplift and rapid basin restriction. / Dissertation / Doctor of Science (PhD)