We show that post-depositional formation of iron(II) phosphate as vivianite strongly alters the phosphorus record in sediments of the Bornholm Basin (Baltic Sea). These minerals began to precipitate in the lake sediments just after the last lake–marine transition ~ 7.5 kyr BP, migrated downwards and are now a stable feature. Formation of vivianite may affect sedimentary phosphorus records in other systems as well. This should be considered when using such records to reconstruct past environments.