Due to global changes and high-intensity human activities, serious environmental problems (e.g., the advance of the dry season in Lake Dongting wetlands, the continuous decline of water levels in dry season, and the reduction of shallow water depressions) have led to the large-scale extinction of submerged plants in Lake Dongting wetlands in the recent years. In-depth study of the effect of low water level on the growth of submerged plants in Lake Dongting is of great significance for guiding the restoration of submerged plants. We take the typical submerged plants in Lake Dongting, a typical lake connected to the Changjiang River in China, as a model system, and set up 4 water depth gradients (25, 50, 75 and 100 cm) to simulate the hydrological environment of shallow water depressions in the field where submerged plants are mainly distributed and the responses of the growth, biomass, and enzyme activity of Potamogeton malaianus, Hydrilla verticillata, Vallisneria natans and Ceratophyllum demersum to changes in depth. The results showed that: (1) The nutrient content in the early stage was 0.09% of total nitrogen, 0.09% of total phosphorus, 3.04% of total potassium, 20.87 mg/kg of alkaline nitrogen, 10.7 mg/kg of available phosphorus, 326.67 mg/kg of available potassium, 6.97 mg/kg of nitrate, 6.59 mg/kg of ammonia nitrogen, 1.21% of organic carbon, and 2.09% of organic matter. After 2 months, the nutrient content of different bottom water levels was different. The nutrient content of 100 and 75 cm pools was higher than that of 50 and 25 cm pools. Ammonia nitrogen, organic matter and organic carbon contents of 25 cm pool were highest; (2) The 75 cm water level is suitable for the growth of P. malaianus and H. verticillata, and it is suitable for the growth of V. natans and C. demersum; (3) Under different water level conditions, 100 cm water level is conducive to the reproduction and biomass accumulation of P. malaianus. The 75 cm water level is conducive to the reproduction and biomass accumulation of H. verticillata and C. demersum, and the 50 cm water level is beneficial to the reproduction and biomass accumulation of V. natans; (4) The submerged plants at 100 cm water level have strong enzyme activity, followed by submerged plants at 75 and 50 cm water levels, and submerged plants at 25 cm water level are weakest. The results indicated that water level greatly influenced the growth characteristics and biomass accumulation of four submerged plants. We concluded that restoration of submerged plant populations in the water level of 50-100 cm should be considered in the ecological restoration of waters. It is conducive to the promotion of population biomass and restoration of aquatic ecosystems.