Carbon (C) and nitrogen (N) metabolism are essential for the growth and maintenance of submersed macrophytes. They are affected by nutrient and light availability and seasonal changes. In this study, we investigated the changes of C/N metabolism and growth of three natural submersed macrophyte populations (i.e., each in a different site), Potamogeton maackianus, in response to water depth gradients with 0.5 m interval in a freshwater lake for four seasons. Changes were identified by measuring the biomass of the sampled macrophytes and metabolite contents of soluble carbohydrate (SC), starch, and free amino acid (FAA) in their organs. Results showed that no significant and consistent changes were found in the SC and FAA contents in leaves and stems from 1.0 m to 5.5 m water depth, as compared to previous results of controlled studies, suggesting a relative stable C/N metabolism in response to the depth gradients in studied natural populations of P. maackianus. The metabolite contents with the most variations appeared mainly because of seasonal changes. The metabolite contents of the macrophyte populations were more closely correlated with the chemical parameters than with the light parameters in water columns. No significant correlations were found between the metabolite contents with the light attenuation coefficient ($K$) and Secchi depth (SD) in water columns. The NO3-N and total phosphorus (TP) contents in water columns were positively correlated with the SC and starch contents in leaves, respectively. The NH4-N content in water columns was negatively related to the FAA content in leaves. Metabolite contents had weak correlations with depth gradients and light parameters, probably because of the physiological integration among individuals by developed stolons and the canopy-forming characteristic of this species. Our results highlighted the importance of water quality to the C/N metabolism in natural population of submersed macrophyte. (C) 2017 Elsevier B.V. All rights reserved.