In this study, the spatiotemporal distributions, potential sources, and ecological risks of Hg, Cr, and As in seawater, and Hg, As, Zn, Cd, Pb, and Cu in sediments from Daya Bay were investigated. The five-year average concentrations of Hg, Cr, and As in seawater were 0.020 μg/L, 0.79 μg/L, and 2.08 μg/L, respectively. The five-year average concentrations of Hg, As, Zn, Cd, Pb, and Cu in surface sediments were 0.04 mg/kg, 7.34 mg/kg, 63.81 mg/kg, 0.23 mg/kg, 25.60 mg/kg, and 11.78 mg/kg, respectively. Annual variations in Hg, Cr, and As in seawater exhibited different trends. HMs in sediments, such as As, Zn, Pb, and Cu, exhibited similar annual variations, whereas Hg and Cd exhibited different annual variations. The spatial distribution of metal species in seawater and sediments showed significant variability, and the concentrations decreased gradually from the coast to the open sea. The comprehensive potential ecological hazard index (RI) of HMs in sediments indicated a relatively high risk, especially for Hg and Cd contamination. The geoaccumulation indices (Igeo) of As, Zn, Pb, and Cu suggested that these metals did not pollute Daya Bay, whereas those of Cd and Hg indicated mild and moderate pollution. The environmental fates of HMs were discussed based on Pearson correlation analysis, revealing that concentrations of HMs were greatly affected by parameters, such as pH, salinity, dissolved oxygen (DO), and total organic carbon (TOC). Principal component and factor analyses indicated that Hg, Cr, As, and dissolved inorganic nitrogen (DIN) in water originated from similar sources, including domestic sewage and wastewater from fishing ports, runoffs, and outlets. For sediments, it was proposed that Cu, Zn, As, Pb, and TOC exhibited similar sources, including cage culture and waste discharge from outlets. Meanwhile, Hg and Cd originated from other point sources, such as a harbor. The study suggests that sustainable management and economic development be integrated to control pollutant emissions in Daya Bay.