Water depth is one of the primary factors that affected submerged macrophyte growth. The rosette plant (Vallisneria natans) and canopy plant (Myriophyllum spicatum) are two common submerged macrophyte species in lakes of the middle and lower reaches of Yangtze River, China. The two species differ greatly in morphological characteristics. How the fluctuation of water depth could affect their growth and their competitive patterns remains to be studied. In this study, three water depth levels (0.5 m, 1.5 m and 2.5 m) were established to explore the responses of growth and competitive patterns of the two plant species to water depth under the condition of mixed planting. Our results showed that both macrophyte species favored in moderate water depth (1.5 m) environment, with highest values of plant biomass and relative growth rate (RGR) in this water depth. The biomass and RGR of V. natans in low water depth treatment (0.5 m) were significantly lower than that in high water depth treatment (2.5 m). However, the opposite pattern was observed in M. spicatum, high water depth treatment has a greater repression effect on its growth. The two species showed the similar responses in morphology, with the indictors of the aboveground part (leaf length or shoot length) increased and that of the underground parts (root length) decreased under the stress of high water depth. Moreover, the biomass ratios of V. natans to M. spicatum are gradually reduced with the water depth, indicated that the competitive advantage of V. natans were increased with water depth. Our study indicates that water depth fluctuations in lakes may affect not only the abundance of submerged macrophytes, but also their community structure. In restoration of shallow lakes, our study suggests that the photosynthetic characteristics of the key species (such as V. natans) should be fully considered when adjusting water levels to rebuild submerged macrophytes.