Experimental and field studies were conducted to evaluate the effects of NH₄⁺ enrichment on growth and distribution of the submersed macrophyte, Vallisneria natans L, in lakes of the Yangtze River in China, based on the balance between free amino acids (FAA) and soluble carbohydrates (SC) in the plant tissue. Increase of NH₄⁺ rather than NO₃^– concentrations in the water column caused FAA accumulation and SC depletion of the plant. The plant showed a unimodal pattern of biomass distribution along both FAA/SC ratios and external NH₄⁺ concentrations, indicating that a moderate NH₄-N concentration (<0.3 mg L^–1) benefited the plant, whereas the high NH₄-N concentration (>0.56 mg L^–1) eliminated the plant completely. Therefore, 0.56 mg NH₄-N mg L^–1 in the water column was taken as the upper limit for V. natans in lakes of the Yangtze River basin. The mesocosm experiment showed that at a high external NH₄-N (0.81 mg L^–1), V. natans failed to propagate with a loss of half SC content (5 mg g^–1 DW) in the rhizomes, indicating that the consumption of carbohydrates for detoxification of excess NH₄⁺ into non-toxic FAA significantly diminished carbohydrate supply to the rhizomes. This might consequently inhibit the vegetative reproduction of the plant, and also might be an important cause for the decline and disappearance of the plant with eutrophication. The present study for the first time reports substantial ecophysiological evidences for NH₄⁺ stress to submersed macrophytes, and indicates that NH₄⁺ toxicity arising from eutrophication probably plays a key role in the deterioration of submersed macrophytes like V. natans.