Clonal fragmentation (CF), caused by various disturbances, significantly affects the growth performance of plants. However, little is known about how CF affects the growth of submersed macrophytes facing light limitation and nutrient enrichment, a typically situation found in eutrophic lakes. To examine the effects of CF on Vallisneria natans (Lour.) Hara, a common submersed macrophyte species in warm lakes, we combined three different light intensities (4%, 15%, and 30% natural light) with three different nutrient levels in the water and kept the stolons severed or intact. We found that CF negatively affected the growth of V. natans and that the effect strongly depended on light and nutrient levels. Our comparison between severed and intact plants showed that CF decreased the biomass accumulation under moderate-light conditions, whereas no significant difference appeared at low and high light levels. The negative effect of CF on plant biomass tended to be more significant at moderate and high nutrient levels. The total chlorophyll content decreased with CF at moderate and high nutrient levels when light availability was high. Our study adds new information about the role of CF on the survival and growth of submersed macrophytes in eutrophic lakes.