To assess the potential and develop appropriate techniques for the recolonization of lakeshore vegetation at sites where it had been completely lost, a pilot project was launched at Lake Kasumigaura, Japan. We investigated the species composition and density of the soil seed banks (propagule banks) of lake sediments at nine sites (total area, 65,200 m2) where lake sediments were spread thinly (˜10 cm) on the surfaces of artificial littoral zones. These zones were constructed in front of concrete levees and had microtopographic variations. In total, 180 species, including six endangered or vulnerable species and 12 native submerged plants that had disappeared from the aboveground vegetation of the lake, were recorded during the first year of restoration. The distribution of each restored species at the sites suggested the importance of microtopographic variation for recolonizing species-rich lakeshore vegetation. Furthermore, the origin of the source sediment affected the species composition of the established vegetation.