We quantified the independent impacts of flooding salinity, flooding depth, and flooding frequency on the native species, Phragmites australis and Scirpus mariqueter, and on the invasive species Spartina alterniflora in the Yangtze River Estuary, China. Total biomass of all three species decreased significantly with increasing salinity, but S. alterniflora was less severely affected than P. australis and S. mariqueter. Elevated flooding depth significantly decreased their live aboveground biomass of P. australis and S. mariqueter, while S. alterniflora still had high live aboveground biomass and total biomass even at the highest flooding depth. These findings indicated that S. alterniflora was more tolerant to experimental conditions than the two native species, and an unavoidable suggestion is the expansion of this non-native species in relation to the native counterparts in future scenarios of increased sea-level and saltwater intrusion. Even so, environmental stresses might lead to significant decreases in total biomass and live aboveground biomass of all three species, which would potentially weaken their ability to trap sediments and accumulate organic matter. However, the relatively high belowground-to-aboveground biomass ratio indicated phenotypic plasticity in response to stressful environmental conditions, which suggest that marsh species can adapt to sea-level rise and maintain marsh elevation.