Global climate change models forecast an increase and intensification of extreme flood events in the future. Extreme flooding has profound impacts on functional traits and growth status of submerged macrophytes and the entire ecosystem. Studying the effects of extreme flooding on the growth and development of submerged macrophytes is important for understanding and predicting changes in aquatic ecosystems under the context of climate change. Here, we addressed the dual effects of extreme water level increase and enhanced nutrient loading induced by extreme flood events through setting up four treatments during a 90-day experimental period, including control (water level maintained at 75 cm), two extreme flood regimes (water level increased rapidly from 75 cm to 150 cm on the first day with N and P inputs; the water level increased gradually from 75 cm to 150 cm with N and P inputs), and water level maintained at 75 cm with N and P inputs (the total amount of nutrient input was identical among the latter three treatments). The effects of extreme flooding on the growth, reproductive strategies and biomass allocation of the submerged macrophyte Vallisneria natans were investigated with simultaneous monitoring of phytoplankton, periphyton and nutrient conditions (TN and TP) of the water column. Among the 17 measured indicators of V. natans, only root biomass allocation and sexual reproduction allocation did not change significantly among these four treatments. For the individual effect of water level, both of the two flood regimes (extreme and gradual water level increase) reduced ramet number, leave number, spacer number, total spacer length, maximum root length, number of flowers and fruits, biomass of each organ and the total plant biomass, and promoted the growth of periphyton on artificial stripes compared to the treatment with increased nutrient loading and constant water level. With sudden increase of the water level, the biomass investment in spacers tended to be the lowest, while plant height and the biomass investment in leaves tended to be the highest. For the individual effect of nutrient loading, the significant increase in water column N concentration in the treatment with increased nutrient loading and constant water level promoted the growth of phytoplankton and epiphyton on macrophytes compared to the control treatment. However, in terms of the concentrations of phytoplankton and epiphyton, the shading effect of phytoplankton was relatively greater, which inhibited the growth of plant leaves, roots and spacers, whereas the sexual reproduction biomass remained unchanged. For the pattern of the combined effect of increases in water level and nutrient loading, the combined effect of the two environmental factors would strengthen the effect of water level increase on the growth of submerged macrophytes due to the pulses of nutrient input. The combined effect of the two factors would substantially reduce the biomass of leaves, roots, spacers and sexual organs. Therefore, extreme flooding has a great detrimental effect on submerged macrophytes, including direct effect of water level increase, and indirect effects on the growth and development of submerged macrophytes through promoting phytoplankton biomass.