To directly select submerged macrophytes with high accumulation capability from the field, 24 eutrophic lakes along the middle and lower reaches of the Yangtze River were investigated in the study. These eutrophic lakes have large amounts of heavy metals in both water and sediments because of human activities. The results showed that Najas marina is a hyperaccumulator of As and Cd, Ceratophyllum demersum is a hyperaccumulator of Co, Cr, and Fe, and Vallisneria natans is a hyperaccumulator of Pb. Strong positive correlations were found between concentrations of heavy metals in tissues of submerged macrophytes, probably because of coaccumulation of heavy metals. However, for most heavy metals, no significant correlations were found between submerged macrophytes and their surrounding environments. In conclusion, N. marina, C. demersum, and V. natans are good candidate species for removing heavy metals from eutrophic lakes.