Flooding caused by rising sea levels can influence the biogeochemistry of estuarine wetland ecosystems. We studied the relationships of higher flooding intensity with soil carbon (C), nitrogen (N) and phosphorus (P) concentrations in communities of the native sedge Cyperus malaccensis var. brevifolius Boecklr. in the wetlands of the Minjiang River estuary in China. The aboveground and total biomasses of C. malaccensis were higher in high-flooding habitats than in intermediate- and low-flooding habitats. These differences in plant biomass were accompanied by a lower N:P ratio in the aboveground biomass and a higher N:P ratio in the belowground biomass. Higher intensities of flooding were associated with higher soil N and P concentrations in intermediate and deep soil layers. The higher P concentration under flooding was mainly associated with the higher clay content, whereas the higher N concentration was associated with higher salinity. Flooding intensity did not have a net total effect on soil total C concentration. The positive direct effect of flooding intensity on total soil C concentration was counteracted by its positive effects on CH4 emissions and soil salinity. The results suggest that C. malaccensis wetlands will be able to maintain and even increase the current C, N and P storage capacity of the ecosystem under moderate increases of flooding in the Minjiang River estuary.