The purpose of this article was to study the trade-offs among vegetative growth, clonal, and sexual reproduction in an aquatic invasive weed Spartina alterniflora that experienced different inundation depths and clonal integration. Here, the rhizome connections between mother and daughter ramets were either severed or left intact. Subsequently, these clones were flooded with water levels of 0, 9, and 18 cm above the soil surface. Severing rhizomes decreased growth and clonal reproduction of daughter ramets, and increased those of mother ramets grown in shallow and deep water. The daughter ramets disconnected from mother ramets did not flower, while sexual reproduction of mother ramets was not affected by severing. Clonal integration only benefited the total rhizome length, rhizome biomass, and number of rhizomes of the whole clones in non-inundation conditions. Furthermore, growth and clonal reproduction of mother, daughter ramets, and the whole clone decreased with inundation depth, whereas sexual reproduction of mother ramets and the whole clones increased. We concluded that the trade-offs among growth, clonal, and sexual reproduction of S. alterniflora would be affected by inundation depth, but not by clonal integration.