Eight cruises were conducted on the south Yellow Sea (SYS) from 1998 to 2005. Variations and the potential ecological risk of heavy metals were studied using the survey data collected during October 2003. The metal content (except for As) was high in the central area where the fine grain size sediments were dominant, and low inshore area where more coarse sediments were present. This suggested that grain size was important in determining distributions of heavy metals. In some local areas, other influencing factors, such as organic content, sedimentation rate, burial efficiency and metal's existing form were discussed. The annual averages of metals showed a stable trend with appreciable fluctuations in 8 years. Using potential ecological risk index (E (RI)) to evaluate the integrated pollution effect of heavy metals, 38.7% of the investigated area was in a moderate degree of contamination, while 77.8% was under moderate ecological risk. However, no distinct correlation was found between E (RI) and plankton biomass. In conclusion, the sediment quality of SYS was good, and the ecological risk was low in general.