Heavy metal contamination is an elevating threat to the aquatic environment of estuarine bays. In the present study, surface sediments from Shantou Bay in South China were collected and detected for the concentrations of heavy metals including copper (Cu), zinc (Zn), chromium (Cr), nickel (Ni), cadmium (Cd), and lead (Pb) using ICP-MS. Spatial distribution, temporal trend, and potential ecological risks for the metal pollution were discussed. The results showed that levels of metals generally decreased by the order of Zn > Pb > Cr > Cu > Ni > Cd. Spatial variation of metal contents was observed with an order of Rongjiang River > Niutian Bay > Shanthou Harbor for Zn and Cd. Sediments of the Niutian Bay were observed with higher levels of Cu, Cr, Ni, and Pb. Compared with reported data from the same region at different sampling periods, a low–high–low trend was observed for the concentrations of the six elements, suggesting a great improvement of sediment quality in Shantou Bay. The average I_geo values suggested moderate pollution of Cu, Zn, Pb, and Cd. The potential ecological risks of Cu, Pb, Zn, Ni, and Cr were in low levels. More attention should be paid to the Cd pollution, considering its great values of potential ecological risk index. Our findings provided better understanding of heavy metal pollution in estuarine environments.