The seed banks of three rivers, with different trophic levels in Chaohu Lake Basin, China, were investigated to explore the dynamics of seed bank under the pressure of eutrophication. A total of 60 species from 25 family 43 genera were identified from the seed banks of the three rivers. In the eutrophic Paihe River, the species richness and mean seed density were the highest, followed by the oligotrophic Hangbuhe River and the hypereutrophic Nanfeihe River. Various compositions of three functional group assemblage of hydro-ecotypes were found in different rivers. The dominant and endemic species were aquatic, wetland, and terrestrial species in Hangbuhe River, Paihe River, and Nanfeihe River, respectively. The shift trend of seed bank in three rivers probably presented past vegetation dynamics under the trophic process in the rivers of Chaohu Lake Basin. Seed bank in the river bed might be quickly assessed by its trophic level. Additionally, it might imply that the seed bank with more aquatic species in the oligotrophic river would be a potential seed resource for vegetation restoration of severely degraded river ecosystems.