Three kinds of representative sediments were obtained from a macrophyte-dominated bay (East Lake Taihu) and two algae-dominated regions (Western Lake Taihu and Meiliang Bay). Physiological responses of Vallisneria asiatica to these sediments were compared. Results from 20 days exposures showed no obvious differences in malondialdehyde (MDA) in roots, while the MDA content in leaves of plants exposed to Western Lake Taihu sediment was significantly (p<0.05) higher than those exposed to the other two sediments. In comparison to the other two sediments, plants exposed to Western Lake Taihu sediment showed significantly lower (p<0.05) superoxide dismutase in roots and leaves on the 10th and 40th day. On the 40th day, root catalase (CAT) activities in V. asiatica from Western Lake Taihu and Meiliang Bay sediments were lower than that from East Lake Taihu sediment, while leaf CAT activity in V. asiatica from Western Lake Taihu sediment was higher than that from East Lake Taihu sediment (p<0.05). Western Lake Taihu sediment caused more serious oxidative stress in V. asiatica than East Lake Taihu sediment. Results indicated eutrophic sediment was a contributing factor in the disappearance of V. asiatica in Western Lake Taihu.