In order to understand the effects of water and sediment on the growth of submersed macrophyte during eutrophication of waterbody, an experiment was carried out to study the effects of water and sediment from mesotrophic and eutrophic area of Lake Donghu on the growth of Vallisneria natans. Four treatments were designed, including eutrophic and mesotrophic culture conditions, and mesotrophic condition with inorganic nitrogen and phosphorus addition respectively. Indices of the growth experiments included biomass, both the number and length of leaves, number of sprout, were measured. Biochemistry indices including soluble carbohydrate content and free amino acid content were measured. The results showed that biomass, number of leaves and stolen of V. natans were the highest growing in mesotrophic condition, phosphorus addition was the second, and nitrogen addition was the third.The plant in eutrophic condition showed the lowest growth. The results indicted that high trophic condition inhibit the growth of V. natans significantly. Increase of inorganic nitrogen in mesotrophic water inhibited the plant more than did the increase of the phosphorus, suggesting that nitrogen enrichment during eutrophication may be more important than phosphorus for the decline of macrophytes. Soluble carbohydrate and free amino acid contents of V. natans in eutrophic condition were significantly higher than those in mesotrophic conditions, indicating that carbon and nitrogen metabolism of the plant were affected. This might be attributed to excessive accumulation of N in eutrophic waters of submersed macrophyte.