Flevoland (central Netherlands) is an area of long-term discontinuous deposition that has been reclaimed from the Zuiderzee in the 20th century. Before the reclamation, the Zuiderzee had been in a phase of enlargement, threatening inhabitants on the islands and the shores, since the Medieval Period. During this phase, a surficial clay cover was deposited on the island of Schokland (World Heritage Site: Noordoostpolder, northern Flevoland). We have studied the clay sequence in order to reconstruct the island’s flooding history during the last 1200 years. The depositional history of the youngest clay deposit on Schokland is inferred from a literature study, analyses of a digital elevation model, six coring transects, three new 14C accelerator mass spectrometry (AMS) dates and laboratory analyses. The laboratory analyses include thermogravimetric analysis, grain-size end-member modelling (unmixing grain-size distributions), foraminifera, bivalves and ostracods. The geological data were combined with information from historical archives. Together, the results show that a combination of embankments and proximity to the coastline determined the sedimentation history and spatial distribution pattern of the sediment. The results also indicate that sedimentary remains of Late Holocene storm events are still present in the clay deposit on Schokland.