Eutrophication has caused many serious environmental issues in lakes. Submerged vegetation, which plays a key role in maintaining the clear water state of shallow lakes, is strongly influenced by water quality and sediment properties. In this study, we seasonally investigated the water quality, sediment properties and submerged plant communities in 18 sites in Lake Honghu of China, an internationally important wetland under the Ramsar Convention. Results indicated that most of the water quality parameters and sediment properties showed no significant difference among the three site types (i.e., perennially vegetated, seasonally vegetated and unvegetated). However, the Secchi depth in perennially and seasonally vegetated sites was significantly higher that in unvegetated sites. By contrast, season had a strong effect on most of the water quality parameters and sediment properties (e.g., water chlorophyll-a concentration). For submerged vegetation, species richness and biomass showed significant spatial but not seasonal differences, with higher richness and biomass in perennially vegetated sites. Canonical correspondence analysis indicated that the distribution of submerged plants was mainly determined by water NH4+ concentration and water depth. Our findings suggest that restoration of submerged vegetation in Chinese eutrophic lakes may be a feasible method for improving water environments and enhancing ecological functions.