Heavy metal contamination in coastal waters may pose a serious threat to aquatic products and human health. This study aimed to gain a better understanding of the pollution-induced by heavy metals in Haikou Bay and adjacent seas and assessed the potential ecological risk. The spatial distributions of heavy metals including Cu, Pb, Zn, Cd, Cr, Hg, and As were analyzed in the surface and bottom water, surface sediment, and five species of fish collected from Haikou Bay and adjacent seas. For seawater, the results showed that the horizontal distribution of the seven heavy metal elements in the study area had no uniform pattern due to the influence of complex factors, such as land-based runoff, port shipping, and ocean current movement. In contrast, the vertical distribution of these heavy metal elements, except for Zn and Cd, showed high concentrations in the surface water and low concentrations in the bottom water. Due to the symbiotic relationship between Zn and Cd, the distributions of these two elements were similar in the study areas. Different from the complex distribution of heavy metals in water, the highest concentrations of these elements in surface sediment all occurred at station 11 except for Pb. Our study revealed that organic carbon and sulfide are important factors affecting the heavy metal concentrations in the surface sediments. Heavy metals in waters and surface sediment were lower than the quality standard of class I according to the China National Standard for Seawater Quality and the sediment quality, except for Zn in water, suggesting that the seawater and surface sediment in Haikou Bay and adjacent seas has not been polluted by heavy metals. Additionally, the heavy metal As was the main element affecting the quality of fish in this study area, and attention should be paid in the future. The target hazard quotient (THQ) values of seven heavy metal elements in fish were all lower than 1.0, indicating that eating fish in this area will not pose a risk to human health. These results provide valuable information for further understanding the status of heavy metal pollution in Haikou Bay and adjacent seas and the development of targeted conversation measures for the environment and fish consumers.