Understanding how traits and multiple diversity of plant community change along with environment gradient can profoundly reveal the mechanism of environment factors on plant community assembly. Water depth is a critical factor affecting the community assembly of submerged macrophytes in lakes. In this study, we aim to examine how the community weighted functional traits, species diversity, functional diversity and the association of the two facets diversity respond to water depth gradients. We collected the submerged macrophytes samples at 300 sampling points along 10 transects in Nansi Lake, which crossed the water depth of the submerged macrophytes colonized in the lake. Then, we measured nine community weighted functional traits (plant height, branch number, internode number, stem diameter, root length, rhizosphere diameter, aboveground weight/underground weight ratio, specific leaf area and plant phosphorus content), five species diversity indexes (Berger-Parker dominance index, Margalef richness index, Simpson diversity index, Shannon-Weiner diversity index and Pielou evenness index), and five functional diversity indexes (FRic functional volume index, FEve functional evenness index, FDiv functional division index, FDis dispersion index and Rao functional division two-times entropy index) for these samples. The results showed that: (1) community weighted height, root length, rhizosphere diameter, aboveground weight/underground weight ratio, specific leaf area and plant phosphorus content differed significantly among different water depths, while branch number, internode number and stem diameter were not significantly different among different water depths. (2) The submerged macrophytes community at moderate water depths showed the highest species diversity and functional diversity. (3) Correlations between five species diversity indexes and three of the functional diversity indexes (FRic index, FEve index, and FDiv index) were dependent on water depth, while the correlations between five species diversity indexes and FRic index, FDiv index were independent on water depth. Our results suggested that species diversity, functional diversity of the submerged macrophytes in Nansi Lake showed a similar trend in response to water depth gradients, but their associations varied along with water depth. Therefore, simultaneous considering the two facets of diversity would be essential for revealing the mechanism of water depth on submerged macrophyte community assembly.