Adaptations to low light and water depth stresses are crucial for the survival of submerged macrophytes. To determine the phenotypic responses of Vallisneria natans to such stresses, we combined a field investigation, a light control experiment and an in situ response experiment to evaluate adaptive variations in fresh weight and morphological and physiological characteristics. In the field investigation and the light control experiment, water depth and light intensity were the main environmental factors affecting the fresh weight and morphological characteristics of V. natans. Fresh weight and leaf length were the most significant responding variables, and they were positively correlated with water depth and negatively correlated with underwater light intensity, although the root length and leaf number exhibited no variation. The leaf length elongated more rapidly at sites with intermediate water depth and low light intensity, and the allometric slopes were steeper. Furthermore, the in situ response experiment results showed a unimodal distribution of the chlorophyll-a concentrations of V. natans along with increasing water depths (from 0.5 m to 8.5 m). The turning point of the chlorophyll-a concentration occurred at 5.5 m, which is almost the maximum water depth at which V. natans occurs in Lake Erhai. Overall, our results evidenced that light availability is an important driving factor that controls the status of V. natans by affecting not only its morphology and physiology but also its biomass allocation and ramet production. An alternative resource allocation pattern of V. natans could be a shift between light acquisition and clonal reproduction.