Sediment cores were collected from the nearshore to bay mouth region in Daya Bay, aiming to describe the historical patterns of heavy metals deposition in the sediment. During the last 40 years, the heavy metals exhibited significant different deposition behaviors in the sediment, in which As, Zn, Cr were more enriched and contributed to metals pollution in this area. Moreover, heavy metals deposition exhibited completely opposite behaviors from the nearshore to bay mouth region. An increasing of pollution level and ecological risk was observed in the nearshore, whereas a decreasing trend was detected in the bay mouth. Principal component analysis suggested that heavy metals were possibly derived from anthropogenic activities in the nearshore, whereas natural sources were the main sources in bay mouth. The results indicated the urgency of implementing efficient measures to mitigate heavy metals contamination in the adjacent sea.