Aluminate is generally used as a flocculent in water and wastewater treatment processes, but the residual aluminum (Al) may have toxic effects on aquatic organisms when the concentration accumulates beyond a threshold level. The in situ and laboratory tests were conducted to evaluate the impact of residual Al on submerged macrophytes in West Lake, Hangzhou, China, which receives Al flocculant-purified water diverted from the Qiantang River. The responses of Vallisneria natans and Hydrilla verticillata were investigated based on their morphological and physiological parameters in pot culture and aquarium simulation experiments. In the pot culture experiments, the biomass, seedling number, plant height, stolon number, stolon length, and root weight were significantly higher at a site located 150 m from the inlet compared with those at a site located 15 m from the inlet (P < 0.05), thereby indicating that the residual Al significantly inhibited the morphological development of V. natans and H. verticillata. The variations in the chlorophyll-a, protein, and malondialdehyde contents of the two species in both the pot culture and aquarium simulation experiments also demonstrated that the two submerged macrophytes were stressed by residual Al. V. natans and H. verticillata accumulated 0.052-0.227 mg of Al per gram of plant biomass (fresh weight, mg/g FW) and 0.045-0.205 mg Al/g FW in the in situ experiments, respectively, where the amounts of Al were significantly higher in the plants in the treatment aquaria during the laboratory experiments than those in the controls. These results may have important implications for the restoration of submerged macrophytes and ecological risk assessments in Al-exposed lakes. It is recommended that the Al salt concentration used for the control of lake eutrophication should be reduced to an appropriate level.