The Daya Bay is a typical subtropical bay in Southern China, and chronically stressed by heavy metal pollution. The bioaccumulation of heavy metals in Daya Bay ecosystem is still unclear. In this study, heavy metals (Cr, Co, Ni, Cu, Zn, Ag, Cd, Pb) and stable isotopes (δ13C and δ15N) were analyzed in seawater, sediment, and organisms (planktons, benthos and nektons) sampled from Daya Bay in June and December of 2015, in order to illuminate the influences of heavy metals to Daya Bay ecosystem and the basic information of environmental monitoring and risk assessment. Results showed that the major source of matter in the organisms in Daya Bay was originated from the ocean, while the freshwater input was limited. The food chain of Daya Bay was short and the highest trophic level was 3.48. The nekton predators (e.g. fish) in Daya Bay were omnivorous, and preferred benthic feeding habit in the winter. The levels of heavy metals in environment and organisms generally did not exceed the criteria according to the National Agriculture Products and the National Water Quality of China, except Zn and Pb in seawater and Cd in two crustaceans (Oratosquilla oratoria and Oratosquilla interrupta). Cr, Co, Ni, Zn, Cd and Pb were found to be biominimized along the Daya Bay food web. Cu was biominimized in the summer, but this trend was not significant in the winter. There was no significant correlation between Ag concentration and trophic level in both seasons, in contrast, there was a potential biomagnification of Ag in crustacean. Overall, the levels of heavy metals in Daya Bay ecosystems were relatively low, and further attention should be paid to Zn, Ag, Cd and Pb.