A recent bathymetric survey of Lake Constance revealed ~ 170 mounds composed of loosely deposited rocks aligned in a ~ 10-km long chain along the southern Swiss shoreline in a water depth of 3–5 m. The mounds are 10–30 m in diameter and up to 1.5 m high. Over their entire length of occurrence, the mounds are estimated to be composed of ~ 60 million individual boulders, with a total weight of ~ 78,000 t. A ground penetrating radar (GPR) survey showed that the mounds are not linked to the glacial substrate but were rather deposited artificially on the edge of a prograding shelf composed of Holocene lake sediments. Here, we present the results of a coring campaign with four piston cores along a GPR transect across one of the mounds. The cores recovered the full Holocene sedimentary succession all the way into the basal till that is overlain by lacustrine sediments dating back to ~ 14,400 cal. yrs BP. The four cores are merged into a ~ 12.4-m long composite section reflecting continuous sedimentation from the siliciclastic-dominated Late Glacial to the carbonate-rich Late Holocene. The stratigraphic horizon representing the mound’s construction was radiocarbon-dated to ~ 5600–5300 cal. yrs BP, placing them in the Neolithic period. This age was confirmed by radiocarbon dating of wood samples collected during underwater excavation of the mounds. Geochemical analysis of the Holocene sedimentary succession shows generally high carbonate contents (average of 69%). The interval from 5750 to 4950 cal. yrs BP, a part of the mound period, is characterized by a Holocene minimum in carbonate content (average of 57%) and by larger mean grain sizes. Comparing these values to those from a recent surface-sediment depth transect indicates that this was a period of rather low lake levels, which might have favoured mound construction. Correlations to nearby archaeological sites and to the general West-Central European lake-level record indicates that the mounds likely were built during a short phase of low lake levels during a general trend of climatic cooling followed by a lake-level transgression.