Throughout human history, communication and trade have been key to society. Because maritime trade facilitated the rapid transportation of passengers and freight at relatively low cost, harbours became hubs for traffic, trade and exchange. This general statement holds true for the Pergamenian kingdom, which ruled wide parts of today's western Turkey during Hellenistic times. Its harbour, located at the city of Elaia on the eastern Aegean shore, was used extensively for commercial and military purposes. This study reconstructs the coastal evolution in and around the ancient harbour of Elaia and compares the observed environmental modifications with archaeological and historical findings. We use micropalaeontological, sedimentological and geochemical proxies to reconstruct the palaeoenvironmental dynamics and evolution of the ancient harbour. The geoarchaeological results confirm the archaeological and historical evidence for Elaia's primacy during Hellenistic and early Roman times, and the city's gradual decline during the late Roman period. Furthermore, our study demonstrates that Elaia holds a unique position as a harbour city during ancient times in the eastern Aegean region, because it was not greatly influenced by the high sediment supply associated with river deltas. Consequently, no dredging of the harbour basins is documented, creating exceptional geo‐bioarchives for palaeoenvironmental reconstructions.