The protected Tel-Dor coastal embayment in the eastern Mediterranean preserves an unusually complete stratigraphic record that reveals human–environmental interactions throughout the Holocene. Interpretation of new seismic profiles collected from shallow marine geophysical transects across the bay show five seismic units were correlated with stratigraphy and age dates obtained from coastal and shallow-marine sediment cores. This stratigraphic framework permits a detailed reconstruction of the coastal system over the last ca. 77 ka as well as an assessment of environmental factors that influenced some dimensions of past coastal societies. The base of the boreholes records lowstand aeolian deposits overlain by wetland sediments that were subsequently flooded by the mid-Holocene transgression. The earliest human settlements are submerged Pottery Neolithic (8.25–7 ka) structures and tools, found immediately above the wetland deposits landward of a submerged aeolianite ridge at the mouth of the bay. The wetland deposits and Pottery Neolithic settlement remains are buried by coastal sand that records a middle Holocene sea-level rise ca. 7.6–6.5 ka. Stratigraphic and geographic relationships suggest that these coastal communities were displaced by sea-level transgression. These findings demonstrate how robust integration of different data sets can be used to reconstruct the geomorphic evolution of coastal settings as well as provide an important addition to the nature of human–landscape interaction and cultural development.