Elodea nuttallii is the most important submerged macrophyte used in the culture of Procambarus clarkii and Eriocheir sinensis. However, the low-temperature environment in winter significantly affects the growth and development of E. nuttallii, which in turn impacts aquatic plant production and shrimp and crab aquaculture in the following year. In this study, three water depth gradients (50 cm, 100 cm, 150 cm) were set up to explore the effects of different water depths on the growth and physiology of E. nuttallii during the overwintering period (October to March), by measuring temperature, biomass, soluble sugars, and other physiological indicators. The results showed that: 1) When the air temperature exceeded 10 °C, water temperature decreased with increasing water depth; when the air temperature was below 10 °C, water temperature increased with increasing water depth. When the air temperature fell below 0 °C, water temperature stabilized at depths greater than 100 cm. 2) Plant height initially increased with water depth and then stabilized. At the end of the experiment, biomass was ranked from high to low as follows: 100 cm > 150 cm > 50 cm. 3) As water depth increased, the soluble protein content in plants gradually decreased, while soluble sugar content first decreased and then increased, indicating that increasing water depth could effectively alleviate the hypothermic stress. 4) When water depth exceeded 100 cm, hypothermic stress was significantly alleviated, promoting the subsequent growth and development of E. nuttallii. These findings suggest that maintaining a water depth of approximately 100 cm is an effective management strategy for aquatic plants during the overwintering period.