Estuaries are important features on the coastal landscape due to their potential for rich, diverse, and abundant resources. The modern coast of the southeast Mediterranean is largely devoid of estuaries except in rare circumstances where ample sands are delivered to the shore, such as east of the Nile Delta. Whether or not today's condition is reflective of that present during lower sea-levels is greatly speculative in part due to a dearth of high-resolution sub-surface mapping in the shallower (< 45 m) continental shelf. We report here on a multibeam bathymetry and near-surface seismic stratigraphy survey offshore of Caesarea, along the central Israeli coast; within which we find evidence of preserved estuarine sediments in water depths ~45–10 mbsl, both within paleo-channels of the Crocodile and Hadera rivers, and more broadly across the shelf. These water depths correspond to early Holocene dates (~10.5–7.5 ka) which, based on global sea-level curves, was a period of rapid (~1–1.7 cm/yr) sea-level rise. Now-submerged aeolianite ridges (locally referred to as ‘kurkar’), cemented aeolian deposits formed during pre-Last-Glacial-Maximum (LGM) seaward advance (regression) of the coastline, likely provided some offshore barrier for estuarine development. These were insufficient, however, to account for all the estuarine deposition interpreted, leading us to hypothesize that sand-constructed barrier islands were also present as sea-level rose during the Holocene. This supply of sand, clearly greater than what is evident today, could have originated from sea-level rise phase eroding Nile Delta sediments transported northward by littoral currents, or from increased output from local rivers during wetter climatic conditions. We also observe a transition from linear, shore-parallel aeolianite ridge morphology features on land and in shallow water, to nested, arcuate features below ~30 mbsl. Whereas the linear ridges are thought to be coastal foredune remnants abandoned by the retreating shoreline, the arcuate forms resemble fossil parabolic (blowout) dunes. Based on the recent initiation of parabolic dunes on Cape Cod following anthropogenic denudation of forests there, we suggest that climate aridification approaching the LGM could have denuded vegetation along the Israeli coast, enabling parabolic dune formation landward of the coastal foredunes which were later preserved via cementation. Understanding the past landscape of the offshore allows for better reconstruction of dune formation, river channel presence, and identification of habitats conducive to prehistoric human exploitation and settlement.