Heavy metal contamination, particularly vanadium contamination in mining and smelting areas, is a worldwide serious problem threatening the ecological system and human health. The contamination level of vanadium, arsenic, cadmium, chromium, mercury, and lead in sediments and waters in a vanadium mining area in China was investigated in the present study. The behavior of heavy metal uptake by 12 native aquatic macrophytes was evaluated, including 5 species of emergent aquatic plants (Acorus calamus, Scirpus tabernaemontani, Typha orientalis, Phragmites australis, and Bermuda grass), 3 species of floating plants (Marsilea quadrifolia, Nymphaea tetragona, and Eleocharis plantagineiformis), and 4 species of submerged plants (Hydrilla verticillata, Ceratophyllum demersum, Myriophyllum verticillatum, and Potamogetom crispus). Different heavy metal accumulation abilities were found across these macrophytes. Generally, they tended to accumulate higher contents of chromium, and C. demersum showed a particularly higher accumulation capacity for vanadium. The heavy metals were preferentially distributed in roots, instead of translocation into leaves and stems, indicating an internal detoxification mechanism for heavy metal tolerance in macrophytes. In 24-day laboratory hydroponic experiments, the macrophytes had a satisfied phytoremediation performance for heavy metals, when their concentrations were at the microgram per liter level. Particularly, vanadium was effectively removed by P. australis and C. demersum, the removal efficiencies of which were approximately 50%. In addition, a combination of terrestrial plant (Bermuda grass) and aquatic macrophytes (P. australis, M. quadrifolia, and C. demersum) exhibited high uptake capacity of all the six heavy metals and their residual concentrations were 95 (vanadium), 39.5 (arsenic), 4.54 (cadmium), 17.2 (chromium), 0.028 (mercury), and 7.9 (lead) μg/L, respectively. This work is of significant importance for introducing native macrophytes to remove low-level heavy metal contamination, particularly vanadium, and suggests phytoremediation as a promising and cost-effective method for in situ remediation at mining sites.