To understand how Scirpus mariqueter responds to the creek-forming disturbance, we examined the differences in morphology and biomass allocation of the species between creekside and inland communities in the Changjiang estuary. Rhizome length and branching intensity were significantly greater in the creekside communities than in the inland community, and they were positively correlated to each other in both kinds of communities, enabling the clones to colonize a larger area and exploit resources efficiently in the creekside habitats. The plants growing along the creekside decreased substantially in their sexual reproduction and allocated more biomass to corms and vegetative reproduction than the inland ones. The biomass allocation pattern of the creekside clones was assumed to be a conservative strategy adopted by the species under disturbance to enhance survivorship at a clone level. In addition, our results imply that reciprocal translocation of materials between parent and daughter ramets probably occurred in the clones within the creekside communities, indicating that clonal integration may play an important role in controlling the responses of S. mariqueter to disturbance. We concluded that the clonal plant S. mariqueter has a high capacity for tolerating tidal disturbances.