We analyzed the development of submerged macrophytes and seed banks under an intense pen culture since the 1980s in Lake Honghu, China. We determined the relationship between depth distribution of seed banks and the historical dynamics of standing vegetation and evaluated the restoration potential of persistent soil seed banks at an abandoned pen-culture area. Eleven submerged macrophytes were recorded in the standing vegetation during 5 survey years, and mean wet biomass increased from 2760 g m？2 in 1961 to a maximum of 5269 g m？2 in 1992, and then declined to 1157 g m？2 in 2010. Seeds of 8 macrophytes were found in the seed banks in 28 of the 32 sampling sites, with a mean density of 1936 seeds m？2 over the entire sediment profile of 0–40 cm. Significantly more total seeds and viable seeds were present in the non-pen-culture area (2729 and 914 seeds m？2, respectively) than in the pen-culture area (902 and 255 seeds m？2, respectively). Our results showed a straightforward but small quantitative relationship between depth distribution of seed banks and historical variation of standing vegetation, suggesting that the depth distribution of the seed bank was a significant but relatively weak predictor of historical vegetation. The soil seed bank can potentially play an important role in vegetative restoration in the abandoned pen-culture area.