Abstract: Vallisneria natans is a dominant species in lakes connecting the Yangtze River, and is essential in maintaining the structure and function of lake ecosystems. Water depth is the main environmental factor affecting the survival and growth of submerged macrophytes. Too shallow or too deep water condition is not conducive to the stability of submerged macrophytes. In practice, due to the influence of human factors and differences in regional conditions, the water level of many aquatic ecosystems fluctuates to a certain extent, which may have a certain impact on the growth and reproduction of submerged macrophytes, for instance, Vallisneria natans. However, the specific influence of water depth on Vallisneria natans is still unclear. In this study, the population of Vallisneria natans planted after ecological restoration of Lake Pipa of Anhui University was selected as the research object. Three sampling areas with relatively consistent growth condition of Vallisneria natans were selected. In each sampling area, three sampling points were selected according to three different water depth, i.e., 0-10 cm, 10-50 cm, and 50-90 cm (at early stage), and 0-100 cm, 100-150 cm, 150-200 cm (at late stage). In each sampling area, one sample quadrat was set. In each quadrant, the coverage and number of seedlings of Vallisneria natans, the height of mature plants, the length of the longest underground rhizomes, and the number of clones etc., were monitored respectively. Besides, the number of fruit and tuber produced by mature plants of Vallisneria natans was also monitored. Through the methods mentioned above, we could understand the response of typical functional traits of Vallisneria natans to different water depth conditions at different stages of the growth cycle (seed germination, growth and reproduction, etc.). Results show that seed germination and seedling survival rate were negatively correlated with water depth. In addition, with the increase of water depth, plant height, leaf length and specific leaf area increased significantly. Meanwhile, the aboveground biomass ratio of Vallisneria natans was the largest under the deepest water depth. Besides, sexual reproduction of Vallisneria natans was mainly carried out under shallow water condition (0-100 cm, >100-150 cm water depth), while clonal reproduction was mainly carried out by underground tuber under deep water condition (>150-200 cm water depth). The results highlight that the water depth had significant influence on the typical functional traits of Vallisneria natans in the stages of seed germination, growth and reproduction. This study can provide some theoretical support for the protection and recovery of Vallisneria natans population under water level fluctuation.