Seismic high-resolution Chirp profiles from the well-documented submerged Stone Age settlement Atlit-Yam, located off Israel’s Carmel coast, display systematic disturbances within the water column not related to sea-floor cavitation, vegetation, fish shoals, gas or salinity/temperature differences, where flint debitage from the Stone Age site had been verified archaeologically. A preliminary series of controlled experiments, using identical acquisition parameters, strongly indicate that human-knapped flint debitage lying on the sea floor, or embedded within its sediments, produces similar significant responses in the water column. Flint pieces cracked naturally by thermal or geological processes appear not to do so. Laboratory experiments, finite element modelling and controlled experiments conducted in open water on the response to broad-spectrum acoustic signals point to an excited resonance response within human-knapped flint even for sediment embedded debitage, with acoustic signals within the 2–20 kHz interval. The disturbances observed in the water column on the seismic profiles recorded at Atlit-Yam are, therefore, based on these results, interpreted as resonance from human-knapped flint debitage covered by up to 1.5 m of sand. Such a principle, if substantiated by further research, should facilitate efficient and precise mapping of submerged Stone Age sites.