An extensive rescue excavation has been conducted in the ancient harbor of İstanbul (Yenikapı) by the Sea of Marmara, revealing a depositional sequence displaying clear evidence of transgression and coastal progradation during the Holocene. The basal layer of this sequence lies at 6 m below the present sea level and contains remains of a Neolithic settlement known to have been present in the area, indicating that the sea level at ~ 8–9 cal ka BP was lower than 6 m below present. Sea level advanced to its maximum at ~ 6.8–7 cal ka BP, drowning Lykos Stream and forming an inlet at its mouth. After ~ 3 cal ka BP, coastal progradation became evident. Subsequent construction of the Byzantine Harbor (Theodosius; 4th century AD) created a restricted small basin and accumulation of fine-grained sediments. The sedimentation rate was increased due to coastal progradation and anthropogenic factors during the deposition of coarse-grained sediments at the upper parts of the sequence (7th–9th centuries AD). The harbor was probably abandoned after the 11th century AD by filling up with Lykos Stream detritus and continued seaward migration of the coastline.