The large-scale reverse seasonal water-level fluctuation caused by the Three Gorges Reservoir Project has dramatically changed the ecology of draw-down zones leading to degradation of local riparian vegetation. We studied the Wanzhou draw-down zones in the Three Gorges Reservoir Region via field investigations and soil seed bank (SSB) germination experiments. The composition and spatial distribution of the SSB in the planted and natural restored sites revealed the effects of restoration modes on seed bank development and demonstrated responses of SSB composition and structure to water fluctuation. The SSB of planted sites contained 43 species of plants, with a mean seed bank density of 9418.79 seeds/m2, where annual herb species accounted for 57.34%. The SSB at natural restored sites had 38 species of plants, with a mean seed bank density of 6090.09 seeds/m2, where annual herb species accounted for 52.57% of the species. Species diversity was low and annual plants dominated the two restoration sites. SSB species diversity was the highest in mid to upper levels of the draw-down zones. Plantation has increased co-occurrence species of SSB and standing vegetation, and increased their similarity. The number of co-occurrence dominant species of SSB and standing vegetation in planted areas was greater than in natural restored areas. However, the stability of plant communities naturally restored was greater than artificial plant communities as there was a higher proportion of perennials in the SSB with more dominant species similar to standing plant communities. In conclusion, the reverse water-level fluctuation simplified the species composition and shaped the spatial distribution of the SSB at the two restoration sites, and plantation promotes the development both of SSB and vegetation. However, plant communities of the two restoration areas, influenced by water-level fluctuations, will be mainly grasslands dominated by annual plants.