We performed geophysical and geoarchaeological investigations in the Wadden Sea off North Frisia (Schleswig-Holstein, Germany) to map the remains and to determine the state of preservation of the medieval settlement of Rungholt, especially its southern dyke segment, called the Niedam dyke. Based on archaeological finds and historical maps, Rungholt is assumed to be located in the wadden sea area around the island Hallig Südfall. During medieval and early modern times, extreme storm events caused major land losses, turning cultivated marshland into tidal flats. Especially the 1st Grote Mandrenke (or St. Marcellus' flood), an extreme storm surge event in 1362 AD, is addressed as the major event that flooded and destroyed most of the Rungholt cultural landscape. Cultural traces like remains of dykes, drainage ditches, tidal gates, dwelling mounds or even plough marks were randomly surveyed and mapped in the tidal flats by several authors at the beginning of the 20th century. Due to the tidal flat dynamics with frequently shifting tidal creeks and sand bars, the distribution of cultural remains visible at the surface is rapidly changing, making it hard to create a comprehensive map of the cultural landscape by surveying. Today, the Niedam dyke area is fully covered by tidal flat sediments, depriving any remains from further archaeological investigation. Since little is known about the precise location or state of preservation of these remains, our investigation aimed at the rediscovery of the medieval dyke system and associated structure with modern and accurate geophysical, geodetical and geoarchaeological methods. Magnetic gradiometry revealed a large part of the medieval dyke, confirming two tidal gates and several terps connected inland with the dyke, providing a detailed example of a Frisian medieval dyke system. Based on our results, the so far inaccurate and incomplete maps of this part of Rungholt can now be specified and completed. Beyond that, seismic reflection profiles give a first depth resolving insight in the remains of the dyke system, revealing a severe threat to the medieval remains by erosion. The site is exemplary for the entire North Frisian coast, that was influenced by multiple flood events in the middle ages to modern times.