A fossil oyster bed (Ostrea edulis) was recently encountered offshore Helgoland (German Bight). Oysters are important filter feeders in marine environments and their habitat structure supports a large associated biodiversity. The European flat oyster Ostrea edulis has historically occurred in vast populations in the North Sea, but declined massively in the early 20th century. The ecological restoration of Ostrea habitats is a current focal point in the North Sea. To better understand the mechanisms that caused the local collapse of the oyster population, this study investigated the size structure, weight, and age of the shells, along with the spatial dimensions, seafloor properties, and environmental context of the oyster bed. The results show that the demise of the population occurred around 700 CE, ruling out excessive harvest as a driver of decline. Synchronicity of increased geomorphological activity of rivers and concurrent major land use changes in early medieval Europe suggest that increased sedimentation was a viable stressor that reduced the performance of the oysters. The shells provided no indication of a demographically poor state of the oyster bed prior to its demise, but manifested evidence of the wide-spread occurrence of the boring sponge Cliona sp. Our study challenges the assumption of a stable preindustrial state of the European flat oyster in the North Sea, and we conclude that the long-term variability of environmental conditions needs to be addressed to benchmark success criteria for the restoration of O. edulis.