Anthropogenic activities have impacted marine ecosystems at extraordinary scales. Biogenic reef ecosystems built by the European flat oyster (Ostrea edulis) typically declined prior to scientific monitoring. Collating >1,600 records published over 350 years, we created a highly resolved (10km2) map of historical oyster reef presence across its biogeographic range, including documenting abundant reef habitats along the coasts of France, Denmark, Ireland and the United Kingdom. Areal extent data were available from just 26% of locations, yet totalled >1.7 million hectares (median reef size = 30ha, range 0.01 - 1,536,000ha), with 190 associated macrofauna species from 13 phyla described. Our analysis demonstrates that oyster reefs were once a dominant three-dimensional feature of European coastlines, with their loss pointing to a fundamental restructuring and ‘flattening’ of coastal and shallow-shelf seafloors. This unique empirical record demonstrates the highly degraded nature of European seas and provides key baseline context for international restoration commitments.