The study, using ecological stoichiometry theory, is to document how C, N, P, S and Si interact in submerged macrophytes and whether/how they respond to eutrophication. Results showed that submerged macrophytes have relatively low C, Si and N:P. Tissue N, P, S and Si except C coupled well in submerged macrophytes. Tissue N, P, S and Si were relatively more affected by water than sediment. Water depth at which submerged macrophytes stand had strong relationship with tissue C, which supports light:nutrient hypothesis. Based on our results, we concluded that low light and low tissue Si concentration probably are the key factors in determining the fates of submerged macrophytes in eutrophic lakes along the middle and lower reaches of the Yangtze River. We suggest that enhancement of water transparency, is a necessary method to restore submerged macrophytes in turbid and eutrophic lakes.