Aims Myriophyllum spicatum and Hydrilla verticillata are common submerged macrophytes in the Yangtze River basin. To investigate their tolerances and adaptations to water-level fluctuations, an experiment was conducted in a pond. Methods We designed five different amplitudes of water-level fluctuations as static, ±15, ±30, ±60 and ±90 cm during the 74 days of the experiment. In each amplitude treatment, two cultivation methods were examined as monoculture and mixed culture. Important Findings The results showed that M. spicatum had greater morphological responses to water-level fluctuations than H. verticillata. Fluctuating amplitude had significant effects on branch number, shoot length and root dry weight (DW) of M. spicatum, whereas it only had significant effect on branch number of H. verticillata. Both fluctuating amplitude and cultivation method had significant effects on total DW of M. spicatum, which was higher in monoculture than mixed culture. The total DW of H. verticillata was affected by fluctuating amplitude only, and the largest biomass was in the amplitude of ±30 cm. Fruit DW of M. spicatum was largest in the amplitude of ±30 cm, high amplitude of water-level fluctuations would inhibit flowering and seed production. Root DW proportion was significantly affected by fluctuating amplitude and cultivation method in both species, and the root DW proportion of M. spicatum was significantly higher in the amplitude-of ±90 cm. We conclude that moderate amplitude of water-level fluctuations can promote the distribution and growth of both species, and in order to accelerate the restoration of both species in natural habitats, the optimum amplitude should be keep at ±15 to ±30 cm.