Projections of climate change impacts over the coming decades suggest that rising sea levels will flood coastal wetlands, moving the range of wetlands inland from the current coastline. The intensity of flooding in wetland areas will thus increase, with corresponding impacts on soil properties and coastal ecosystems. We studied the impacts of two levels of water inundation on the concentration and stoichiometry of soil carbon, nitrogen, phosphorus and sulfur in areas dominated by the native C3 species Scirpus triqueter L., the native C4 species Cyperus malaccensis var. brevifolius Boecklr. and the invasive Gramineae C3 species Phragmites australis (Cav.) Trin. ex Steud in the Shanyutan wetland areas of the Minjiang River estuary in China. Comparison of the communities dominated by these three species in high- and low-water flood habitats showed that flooding enhanced anaerobiosis and salinity and altered the carbon and nitrogen plant-soil cycles. Higher flooding favored the invasive species more than the two native species. The invasive P. australis accumulated more carbon (65% increase in aboveground biomass), and took up more nitrogen under high flooding than did C. malaccensis and S. triqueter. The more conservative use of soil resources, particularly the limiting nutrient N, appeared to underlie the higher capacity of the invasive species to tolerate higher flooding intensity. Increases in flooding may thus enhance the success and expansion of the invasive P. australis to the detriment of the native plant species in these Chinese wetlands.