Water level fluctuations (WLF), one of the most affected ecological drivers by climate change, are dominant forces controlling submerged macrophyte performance and distribution in freshwater ecosystems. Submerged macrophytes are prominent components of shallow lakes, predicting their response to WLF is therefore crucial for the management and conservation of these valuable and vulnerable ecosystems. We conducted an experiment in 15 outdoor mesocosms to explore the influence of WLF on the performance ofVallisneria spinulosa. We subjectedV. spinulosato WLF of two amplitudes and two frequencies, with stable water level as a control, and measured variations in 20 traits related with growth, sexual and asexual reproduction and resource allocation. Generally, compared with the control plants, fluctuations in water level adversely affected macrophyte biomass and growth, but increased both height and specific leaf area, which are helpful for adaptation ofV. spinulosato high-water level periods. Changes in the WLF frequency had little effect on the growth and reproduction ofV. spinulosaplants apart from their leaf mass. In contrast, increased amplitude not only inhibited aboveground and root growth ofV. spinulosa, but also decreased investment in sexual reproduction by influencing fruit production.V. spinulosaheld a relatively stable allocation to overwintering asexual propagules in response to both components of WFL, which can maintain a capacity for clonal propagation following WLF. Moreover, as WLF amplitude increased,V. spinulosainvested a higher fraction of resources to belowground mass at the expense of their allocation to leaf mass. Our results suggest that shifts in WFL and especially magnified WLF amplitude due to climate change, may severely affect the growth and reproduction of submerged macrophytes with implications for other biota and the ecological state of shallow lakes.