Aquatic plants are an essential component to regulate the physico-chemical environment and microhabitat complexity in the lake ecosystem. Increased risk of eutrophication, land use change, modification of hydro regime, and expansion of invasive species has been projected to change of aquatic plant community composition; however historical pathways of community change were not well recognized in a national scale. We analyzed the temporal change of aquatic plant community from the early 1900s to 2000s using floral record database of 268 lakes in Japan. A total of 131 aquatic plants species (i.e., out of 163 potential aquatic species) were recorded from 396 field survey results. Based on a meta-analysis approach, we tried to identify overall response pattern of different aquatic plant groups (i.e., submerged, leaf-floating, free-floating) against the temporal gradient. Our results will contribute to understand the change of aquatic plants communities in Japanese lake in long-term perspectives and to identify important lake sites for conservation of endangered aquatic plants.