Recurrent water level fluctuation and submergence of plants are common in riparian zones. Our study objectives were to test the independent and interactive effects of submergence level and fluctuation frequency on a globally important riparian invasive plant, Alternanthera philoxeroides. To this end, we conducted a greenhouse experiment, in which ramets of the plants, obtained from a wetland in China, were treated with four fluctuation frequencies (0, 3, 6, and 12 cycles over a 96-day experimental period) under three water levels (0, 10, and 30 cm). We found that effects of fluctuation frequency were non-significant, negative, and positive under water levels of 0, 10 and 30 cm, respectively. As fluctuation frequency increased, the effects of increasing water level decreased significantly. When water levels were high, A. philoxeroides allocated greater biomass to shoot production probably in order to elongate and escape from submergence. However, as fluctuation frequency increased, biomass investment in roots and leaves also increased, probably in order to maximize nutrient absorption and photosynthesis, respectively. These results suggest that water level fluctuation may alleviate the effects of submergence on A. philoxeroides. In addition, A. philoxeroides showed significant phenotypic plasticity, adjusting its functional traits, such as number of nodes and leaves per stem, as well as stem diameter and pith cavity diameter, according to recurrent water level fluctuation. We conclude that A. philoxeroides may perform better in shallow water zones under conditions of disturbance that include recurrent water level fluctuation. This ability to adapt to disturbance likely promotes its growth and invasion in disturbed habitats.