The concentrations of heavy metals (Cu, Zn, Pb, Cd, Cr, Hg, and As) in the sediment which were collected from 17 ponds were determined to clarify their distribution characteristicsand evaluate their ecological risk in aquaculture ponds in Shanghai.Their distribution and sources were analyzed using multivariate statistics, and the ecological risk of heavy metal was assessed by three different methods.The results showed that the average concentrations of heavy metals in the surface sediment were as follows,Zn(58.36±23.41)mg/kg, Cr(41.96±11.92)mg/kg, Cu(20.61±7.76)mg/kg, Pb(10.87±5.83)mg/kg,As(7.81±2.12)mg/kg, Cd(0.13±0.05)mg/kg, Hg(0.055±0.03)mg/kg. There were no significant difference of the annual values of Cu,Zn,Pb,Cr, and As among the sediment from different aquaculture species(P>0.05),while the values of Cd and Hg in the sediment of shrimp and crab ponds were higher than fish ponds obviously (P<0.05). The order of geo-accumulation index (I_geo) of the heavy metals in the sediment were as follows, Cd > As > Cu > Zn > Cr > Hg > Pb, and more than 95%of the samples belong to unpolluted class. The potential ecological risk index (RI) of the heavy metals were 56.94, 76.51, and 69.65 in the sediment of fish, shrimp and crab ponds, respectively. They were all ranged to the low ecological risk grade.Evaluations of consensus-based sediment quality guidelines (CBSQGs) showed that the mean probable effect concentration quotients (M_PEC-Q) of samples were all lower than 0.5, which means that the combined effects of heavy metals in the sediment were not toxic.