Trace element balance is a key parameter in ecological stoichiometry. However, little is known about trace element stoichiometry of submerged macrophytes. We hypothesized that lake nutrients (N and P) and taxonomy strongly affect tissue trace element (Al, As, Ba, Cd, Co, Cr, Li, Pb and Sr) composition and homeostasis of submerged macrophytes in Yangtze floodplain lakes and Yunnan plateau lakes (China). Submerged macrophytes had Co stoichiometric homeostasis in these two sets of lakes. Moreover, submerged macrophytes in Yangtze floodplain lakes had higher Cd stoichiometric homeostasis, whereas submerged macrophytes in Yunnan plateau lakes had higher Cr, Li and Pb stoichiometric homeostasis. Lake nutrients altered trace element composition of submerged macrophytes as shown by canonical correspondence analysis (CCA). Total nitrogen in water (WTN) positively correlated with tissue As and tissue Cd for all lake types, indicating WTN influenced the concentration and composition of tissue As and tissue Cd in submerged macrophytes. Canonical discriminant analysis (CDA) successfully discriminated among submerged macrophyte taxa, revealing there are significant differences in multielement composition of submerged macrophytes among taxonomy. Some similar relationships of taxa and trace elements between Yangtze floodplain lakes and Yunnan plateau lakes indicated that certain families of submerged macrophytes accumulate specific elements. Differences in relationships of taxa and trace elements between Yangtze floodplain lakes and Yunnan plateau lakes indicated that trace element composition of submerged macrophytes could be affected both by taxonomy and the ambient environment.