Abstract Coastal areas can contain a highly valuable archaeological record because of post‐glacial drowning of previously inhabited land surfaces. Such records are increasingly under threat because of a range of economic activities. Archaeological Heritage Management (AHM) is hampered by a lack of detailed data on the buried landscapes. This makes it difficult to fully assess and deflect threats to this record. Here, we present a novel way of using under water magnetometer surveys to map and characterize buried Mesolithic/Neolithic landforms in high detail. Magnetometer maps from the IJsselmeer area (Netherlands) show patterns of paired linear anomalies that resemble banks or levees that straddle channel‐like features. Sub‐bottom profile transects and sediment core analyses confirm that the observed linear features are Mesolithic and Neolithic submerged buried channel and bank/levee systems that connect to known onshore buried channel systems from that age. Although the origin of the magnetic signal is still subject of study, the observed patterns clearly indicate areas or geomorphological phenomena of high archaeological potential, and make it possible to take measures for protection and research.