The current work investigated the potential of submerged macrophyte pondweed (Potamogeton malaianus) in treating cadmium, nickel, and lead‐contaminated water through phytoremediation. The adsorption for the three metal ions occurred rapidly within 2 h and attained dynamic equilibrium in no more than 72 h. The removal efficiencies of Cd (II), Ni (II), and Pb (II) were high, passing 94% in both single‐ and multi‐metal systems. The kinetic adsorption curves of Cd (II), Ni (II), and Pb (II) were fitted well by both pseudo‐first‐order and pseudo‐second‐order kinetics (R2 = 0.9875–0.9995). The equilibrium adsorption capacities of Cd (II), Ni (II), and Pb (II) for P. malaianus were 6.29–6.97 mg kg−1. In plants, the higher concentration of each metal ions was accumulated in leaves (12.44–38.15 mg kg−1) than in roots (10.32–26.10 mg kg−1). The chlorophyll contents increased from 0.69 to 0.89–1.00 mg g−1 under the treatment of Cd (II), Ni (II), and Pb (II), whereas the chlorophyll a/b ratio was kept constant. There was no significant difference between single‐ and multi‐metal systems. FT‐IR spectra showed that COH and C═N might be involved in the adsorption of Cd (II), Ni (II), and Pb (II). This study demonstrated that P. malaianus could be a suitable submerged macrophyte for the simultaneous removal of Cd (II), Ni (II), and Pb (II) from water.