During the early Holocene, rapid sea level rise led to the inundation of worldwide coastal areas, with the surrounding shallow landscapes being the most affected. The Carmel coast, located in the East Mediterranean, preserves a rich record of such a submerged landscape dotted by many archaeological sites, including the well-preserved Atlit-Yam village (Neolithic), which is currently buried and submerged at 8-11 m water depth. In order to reconstruct the geomorphological evolution of the submerged landscape, 23 sediment cores of variable length (ranging 60-240 cm) were drilled both inside and outside the known extent of the Atlit-Yam village. A detailed stratigraphy of the submerged landscape was generated based on the analysis of 18 out of 23 cores, framed by robust radiocarbon ages. The sedimentary sequences identified in the analyzed cores were defined by respective facies associations, and combined with physical (grain size, magnetic susceptibility), chemical (elemental geochemistry), and organic (total organic content) properties of the sediments. Our analysis reveals a non-uniform evolution of submerged coastal sediments, influenced by sediment supply, regional geomorphology, and human activity. Within a spatial stratigraphy, we found distinct anthropogenic units that underlines the intricate balance between humans and the Early Holocene changing environment (including sea level rise, depositional processes, and sediment dynamics). This study holds implications for future research in identifying and preserving potential archeological sites elsewhere and helps to shed light on the impact of climate change, sea level, and surface processes on coastal communities.