The water level fluctuation zone (WLFZ) has experienced a novel hydrological regime due to the anti-seasonal operation of China's Three Gorges Reservoir. Overall, hydrological change can significantly influence the riparian environment and shift the riparian vegetation. Although numerous studies have investigated the short-term responses of riparian plants to water level fluctuation in this zone, few have addressed long-term effects. In this study, four permanent plots in the WLFZ of the canyon landform area were chosen to evaluate the long-term responses of riparian plants to water level fluctuation from 2008 to 2015 and to screen candidate plants for ecological restoration. We recorded 146 species in 2008, 110 species in 2009, 68 species in 2012 and 69 species in 2015, indicating a conspicuous loss in riparian plants. Most of the remnant plants were annual and perennial herbs. Of the native species present in 2008, 82, 22 and 8 had disappeared in 2009, 2012 and 2015, respectively. Simultaneously, 45, 15 and 11 non-native species were first found, respectively. Additionally, over half of the native and the non-native species were not found after being subjected to a water level fluctuation. From 2008 to 2015, only 27 native species always presented; however, not all of them were chosen as candidates for ecological restoration because of their decreased importance values. In contrast, the importance value of Cynodon dactylon increased over time, suggesting its high tolerance to long-term winter flooding. We concluded that riparian plants' composition of the canyon landform area dramatically declined after long-term water level fluctuation and their presence was determined by the novel hydrological condition. Our results also suggested that Cynodon dactylon or its combination with other species (i.e. Digitaria chrysoblephara, Setaria glauca, Setaria viridis) is a better candidate for ecological restoration in the WLFZ.