Fluctuations in relative sea level, tectonic movement, and sedimentation during the late Pleistocene to Holocene in the Hisarönü Gulf (SE Aegean Sea) and surrounding area were investigated with a high‐resolution geophysical survey and underwater archaeological observations. The Hisarönü Gulf has been affected by vertical tectonic movements and rising sea level following the last glacial period (20,000 yr B.P.). High‐resolution seismic data were interpreted to reveal the structure of the late Pleistocene to Holocene deposits and determine the location of the paleoshoreline. In order to describe the relative rise of sea level, principles of sequence stratigraphy were used for the late Pleistocene to Holocene transition, and submerged archaeological remains and bioerosional indicators were used for the late Holocene period. A comparison of archaeological observations in the study area with the known regional sea level curve indicates that the relative rise in sea level for the late Holocene is, for the most part, due to the tectonic subsidence of the coastal plain. © 2012 Wiley Periodicals, Inc.