The investigation of submerged archaeological sites faces numerous logistical challenges in the recovery of stratigraphic sequences and, as a result, is often restricted to surface deposits limiting the application of geoarchaeology. This paper outlines a new integrated field and microanalytical methodological protocol to investigate deep stratigraphic sequences (up to 2 m) within the submerged Pre-Pottery Neolithic (PPN) site of Atlit-Yam (9267-7970 cal. B.P. [calibrated years before the present]). A new coring method for the extraction of deep underwater stratigraphy was developed to extract three cores: two between architectural remains within the site and one outside the site. The cores were analysed using Fourier-transform infrared spectroscopy, phytolith and pollen analysis and archaeological micromorphology to detect anthropogenic signals and undertake paleoenvironmental reconstruction. Our results indicate anthropogenic evidence at 95 cm depth based on the presence of heat-altered sediments, high phytolith concentrations and micromorphological observations of archaeological remains. Radiocarbon analysis indicates the oldest anthropogenic layers date to the Mid Pre-Pottery Neolithic B (PPNB) and Late PPNB (9859-9323 cal. B.P.), bearing implications for reassessing the emergence of the first coastal Neolithic villages in the Mediterranean. Our integrated field and multiproxy micro-geoarchaeological protocol offers a new approach to detecting and studying submerged archaeological sites worldwide.