Phenotypic plasticity is an important adaptation to spatial and temporal environmental variations. For submerged macrophytes, adaptation to water depth and light variation is particularly important. To determine the morphological and physiological adaptive strategies of Vallisneria natans at different water depths and light conditions, we combined field investigation, light control experiment and in situ physiological response experiment. In the field investigation and the light control experiment, both water depth and light intensity had prominent effects on the morphological of V. natans, especially in fresh weight and leaf length. The leaf length elongated more rapidly at intermediate water depth sites with lower light intensity. In the in situ experiment, the survival boundary of V. natans is 5.5 m in Lake Erhai. Below this depth, the chlorophyll-a content increased gradually with increasing water depth. Our results demonstrated that V. natans can adapt to water depth and light availability by changing morphological, physiological and resource allocation. At low light condition, V. natans invested more resource for light acquisition, simultaneously, changing the photosynthetic pigment content to compensate for light attenuation; conversely, more resource was directed towards reproduction. These results will provide new insight for species selection when conducting aquatic plants restoration in freshwater ecosystem.HIGHLIGHTSWater depth and light availability affect the morphology, physiology, and resource allocation of V. natans.An alternative resource allocation pattern of V. natans could shift between light acquisition and reproduction.