The accumulation of trace metals in aquatic organisms may lead to serious health problems through the food chain. The present research project aims to study the accumulation and potential sources of trace metals in aquatic organisms of the Pearl River Estuary (PRE). Four groups of aquatic organisms, including fish, crab, shrimp, and shellfish, were collected in the PRE for trace metal and Pb isotopic analyses. The trace metal concentrations in the aquatic organism samples ranged from 0.01 to 2.10 mg/kg Cd, 0.02 to 4.33 mg/kg Co, 0.08 to 4.27 mg/kg Cr, 0.15 to 77.8 mg/kg Cu, 0.17 to 31.0 mg/kg Ni, 0.04 to 30.7 mg/kg Pb, and 8.78 to 86.3 mg/kg Zn (wet weight). High concentrations of Cd were found in crab, shrimp and shellfish samples, while high concentration of Pb was found in fish. In comparison with the baseline reference values in other parts of the world, fish in the PRE had the highest elevated trace metals. The results of Pb isotopic compositions indicated that the bioaccumulation of Pb in fish come from a wide variety of food sources and/or exposure pathways, particularly the anthropogenic inputs.