This dataset has compiled to provide a comprehensive database of macrophytes, along with lakes and survey information from the literature, to provide a historical record macrophyte biodiversity for lakes in Japan. The present data contains occurrence records of 2,779 taxa, of which 2,689 have been identified at species/infraspecies (forma, variety, and subspecies), whereas the remaining 90 taxa could only be identified at the section, subgenus, genus, or higher taxonomic ranks. The taxa consisted of 2,474 angiosperms, 33 gymnosperms, 138 pteridophytes, 45 bryophytes, and 89 algae, including green algae (charophytes, zygnematophytes, and Chlorophyta), red algae (Rhodophyceae), and brown algae (Phaeophyceae). This dataset is published as a data paper in Ecological Research (see https://doi.org/10.1111/1440-1703.12449).