Nutrient availability can affect both the morphology and the nutrient uptake strategies of submerged macrophytes, with different species responding differently to increases in nutrient levels. A 98-day mesocosm experiment was conducted to investigate the responses of co-cultured Hydrilla verticillata and Vallisneria natans to nutrient enrichments of 3.0 mg N/(L ∙ week) and 0.2 mg P/(L week), mimicking external loading. Water samples were collected every 2 weeks for measuring nutrient and total suspended solid (TSS) concentrations and biomass of phytoplankton (Chl a). Dry biomasses of roots and shoots of both species were measured at the end of the experiment. Results showed that under nutrient-enriched conditions, both species reduced the ratio of root to shoot growth and increased nutrient storage per unit of biomass. However, only H. verticillata exhibited enhanced growth and nutrient storage, as well as a lower root: shoot ratio and greater shoot biomass than seen in Vallisneria. Our findings demonstrate that nutrient enrichment of the water column can invoke morphological plasticity in both H. verticillata and V. natans, but when both species grow together, the growth advantage goes to the former.