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This dataset is based on the Atlas of Freshwater Bivalves in Mainland Portugal published by ICNF in 2006. It presents occurrence data of native and exotic freshwater bivalves on water bodies in hundreds of sampling stations at Mainland Portugal, from 2001 to 2004. There are records of 12 native species and one exotic with confirmed occurrence in Portugal, namely Corbicula fluminea (O. F. Müller, 1774). The project "Atlas of freshwater bivalves in mainland Portugal" was coordinated by Joaquim Reis and involved the participation of several individual and institutional collaborators.