Here, we describe an experiment using four nitrogen (N) and phosphorus (P) concentrations to investigate the effects of nutrient enrichment on the submersed macrophyte Vallisneria natans (tape grass) grown in a sand culture medium. The objective of this study was to examine the influence of nutrient enrichment in the water column on V. natans, especially with regard to anatomical structures. The results showed both the absolute growth rate (AGR) and intrinsic efficiency of light energy conversion of PSII (Fv/Fm) decreased with increasing nutrient levels. Root morphological characteristics, including the total root length (L), root surface area (SA), projected root area (PA), total root volume (V), average root diameter (AD), total root length per volume (LPV), total tips (T) and total forks (F), also showed a generally negative relationship with increasing nutrient concentrations. The anatomical structures of stolons and leaves also changed with nutrient enrichment. The shrinkage of aerenchyma and disappearance of starches and chloroplasts were the main structural changes leading to poor growth. These phenomena, especially the anatomical changes, might be the mechanism underlying the effect of nutrient enrichment on V. natans growth.