Dataset in support of the publication "Shellfish reefs increase water storage capacity on intertidal flats over extensive spatial scales" published in Ecosystems, bij Nieuwhof, Van Belzen, Oteman, van de Koppel, Herman and van der Wal. It includes the data and scripts (R and matlab) for the analyses and figures in this publication. This includes aerial images and elevation maps of the 3 shellfish reefs studied and calculated water storage capacity of the reefs. It also includes a map of water storage capacity of the Dutch Wadden Sea south of the island of Schiermonnikoog based on a bathymetry map.