Four kinds of sediment heavy metal samples (Zn, Cu and Pb and Cd ) were collected from lakes, rivers, and aquaculture ponds in Kunshan for analysing distribution pattern and evaluating pollution status of these sediment heavy metals . The results show that, the Cu value at sampling sites of lakes varied between 6.54-333.99 mg/kg, and the mean value was136.60 mg/kg. The Cu value at sampling sites of rivers varied between 11.00-475.88 mg/kg, and the mean value was 126.78 mg/kg. The Cu value at sampling sites of aquaculture ponds varied between 31.73-155.78 mg/kg and the mean value was 84.73 mg/kg. The ecological risks of these four heavy metal elements in Kunshan waters was Cu > Cd > Zn > Pb. The potential ecological risk index of Pb, Zn, Cu was under 40. It showed the three kinds of heavy metals were at low ecological risk. And the potential ecological risk indexes of Cd all exceed 320. What’s more, the potential ecological risk indexes of Cd in all sites were more than 600,and present serious ecological risks. The general potential ecological risk level of heavy metals was in the order: aquaculture ponds > lakes > rivers.