With the filling of the Three Gorges Reservoir, original vegetation in the water level fluctuation zone (WLFZ) between the elevations of 145 and 175 m disappeared due to the reversal of submergence time (winter flooding) and prolonged inundation duration (nearly half a year). To better understand the relationships between the environmental factors and recovered plant communities for reconstructing floristically diverse riparian zone, we conducted a field survey in 11 sites in the WLFZ in June 2010, and vegetation composition, flooding characteristics, heavy metals, and soil major nutrients were determined. Consequently, the canonical correspondence analysis was used to investigate the relationships between plant species composition and flooding characteristics, heavy metal contamination, and soil nutrients. Results demonstrated that vegetation in the WLFZ was dominated by annuals, i.e., Echinochloa crusgalli and Bidens tripartita, and perennials including Cynodon dactylon, and plant species richness and diversity were negatively associated with flooding duration, heavy metal contamination, and nutrients including total phosphorus, available phosphorus, available potassium, and nitrate. Our results suggest that plant species, recovering mainly through soil seed bank and regeneration of remnant individuals, have been influenced by the combined effects of environmental factors.