Shell middens, or shell-matrix deposits, occur in large numbers across the coastlines of the world from the mid-Holocene (ca. 6000-5000 cal BC) onwards, often forming substantial mounds. However, they become smaller, rarer or absent as one goes back into earlier periods, suggesting a worldwide process of economic intensification. Since sea level was generally much lower during these earlier periods, a critical question is the extent to which mounded shell middens could have accumulated on now-submerged palaeoshorelines, and if so, how they were affected by the potentially destructive impact of sea-level rise. Further, and important to modern practice, it is essential that archaeologists consider how such sites can be discovered through underwater investigation. Here we offer a proof of concept that shell middens can survive submergence and can be detected, using systematic investigation of a rare example of a confirmed underwater shell midden at the Mesolithic site of Hjarnø (ca. 5300-4300 cal BC) in Denmark. We