As we know, the survival of young ramets and stolons is essential for the clonal growth of many aquatic plants. However, few NH4+ enrichment experiments on clonal growth of submerged macrophytes have been conducted to provide possible evidences for their declines in eutrophic lakes. Here, the growth and physiological responses of V. natans to the enrichment of NH4+-N were examined under six inorganic nitrogen (IN, i.e., the sum of nitrate nitrogen (NO3--N) and ammonium nitrogen (NH4+-N)) concentrations (control, 2.5, 4.5, 6.5, 8.5, and 10.5mgL(-1)). When NH4+-N concentration increased over 0.5mgL(-1), free amino acid (FAA) contents in leaves and stolons increased while soluble carbohydrate (SC) and starch contents decreased, and major growth indices (total biomass of plants, number of ramets, and stolon dry weight (DW)) also showed a degressive tendency. Remarkably, the stolon DW significantly declined with increasing FAA, but significantly positively related to SC and starch. These results indicated that clonal growth of V. natans was inhibited by high NH4+-N concentration, and imbalance of C-N metabolism of stolons partly explained the decline of submerged clonal macrophytes. In this study, the leaves of new and small (NS) ramets contained significantly more FAA and less SC than that of mature and mother (MM) plants, indicating that the C-N metabolism of young ramets was easier to be disrupted, consequently inhibiting the clonal growth of aquatic plants. Furthermore, under the condition of high NH4+-N concentration, FAA may be a useful indicator of both macrophyte growth and physiological stress of plants.