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Coastal landscapes are sensitive to changes due to the interplay between surface and submarine geological processes, climate variability, and relative sea level fluctuations. The sedimentary archives of such marginal areas record in detail the complex evolution of the paleoenvironment and the diachronic biota response. The Elefsis Bay is nowadays a landlocked shallow marine basin with restricted communication to the open Saronikos Gulf. A multi-proxy investigation of a high-resolution sediment core recovered from the deepest part of the basin offered a unique opportunity to record the paleoenvironmental and aquatic ecosystem response to climate and glacioeustatic sea level changes since the Late Glacial marine transgression. The retrieved sedimentary deposits, subjected to thorough palynological (pollen, non-pollen palynomorphs, dinoflagellates), micropaleontological (benthic foraminifera, calcareous nannoplankton, ostracods), and mollusc analyses, indicates isolation of the Elefsis Bay from the Saronikos Gulf and the occurrence of a shallow freshwater paleolake since at least 13,500 cal BP, while after 11,350 cal BP the transition towards lagoon conditions is evidenced. The marine transgression in the Elefsis Bay is dated at 7500 cal BP, marking the establishment of the modern marine realm.