The results of the analysis of the groundstone items recovered from the submerged Pre-Pottery Neolithic C site of Atlit-Yam are presented, and the assemblage compared to those from the inundated Late Pottery Neolithic/Early Chalcolithic (LPN/ECH) sites of Neve Yam and Tel Hreiz. Based on previous studies, a specific typology for groundstone artifacts was established for the Atlit-Yam site. Our observations include 30 parameters for each artifact according to which the artifacts were sorted into types and subtypes. The production techniques and choice of raw material were characterized, and the possible function and use of the implements identified. The most common raw material is limestone with negligible use of basalt, which is opposite to the trend found at Neve Yam and Tel Hreiz. At Atlit-Yam coarse limestone was used only for the manufacture of grinding tools, as a substitute to basalt—perhaps reflecting changes in trade networks over time. Groundstone containers (cupmarks and bowls) are abundant at Atlit-Yam but few at Neve Yam, probably reflecting the introduction of ceramic vessels in the later LPN/ECH period. Moreover, grinding implements are more common at Neve Yam than at Atlit-Yam, possibly reflecting a greater reliance on agriculture at the former site.