The purpose of this study was to analyse the distribution of heavy metal concentrations of Hg, Pb, and Cr in the coastal waters of Ternate Island. There are 10 sampling points, each 4 sampling points around fishing boat docks, 2 sampling points around settlements, and 4 sampling points around Pertamina's Port. Heavy metal analysis of Hg, Pb, and Cr was carried out on seawater and sediment samples using atomic absorption spectrophotometry (AAS). The measurement of the physical-chemical parameters of the waters obtained that the average of each parameter was temperature 30.39 °C, salinity 30.33 ‰, pH 7.88, dissolved oxygen (DO) 11.54 mg/l, total dissolved solids (TDS) 35.02 mg/l, and organic carbon dissolved 62.65 mg/l. The physical-chemical parameters of the waters at this research site were still good for the survival of marine organisms. Sediment texture indicated that the dominant sediment texture at the research site was sand. The average concentrations of heavy metals Hg, Pb, and Cr in the seawater were 0.00085 mg/l, 0.01 mg/l, and 0.045 mg/l, respectively. Concentrations of heavy metals Hg in the seawater was in accordance with quality standards, while heavy metals Pb and Cr have exceeded water quality standards (Government Regulation Number 21 of 2022). The average concentrations of heavy metals Hg, Pb, and Cr in the sediment were 0.390 mg/kg, 15.66 mg/kg, and 14.02 mg/kg, respectively. Based on the Canadian Council of Ministers for the Environment (CCME, 2001), concentrations of heavy metals Pb and Cr in sediments were below the threshold for the marine biota protection while Hg has exceeded the threshold. Each heavy metal has unique characteristics and a distinctive distribution pattern controlled by physical-chemical processes that occur in the marine systems so that studies of heavy metals from each region globally are always required.