Heavy metal contamination in the estuarine wetlands of tropical islands is becoming increasingly severe. This study focused on four typical estuarine wetlands of Hainan Island, including the mangrove and seagrass areas in Lingshui County, the mangrove and seagrass areas in Xinying Port, the mangrove area in Sibi Wan, and the seagrass area in Huachang Wan. By analyzing the heavy metal content in the surface sediments of these wetlands, we investigated the distribution characteristics and levels, explored their influencing factors, and assessed ecological risk of heavy metals in these areas. It was found the accumulation of heavy metals was high from obvious sampling sites of human activities, the type of sediment could affect the adsorption of heavy metals, with silty mudflats accumulating more. TOC/TN indicated that the organic sources of mangroves were diverse, included environmental impacts and human interference. According to the soil accumulation index and potential ecological risk index in these areas, almost all heavy metals were unpolluted except for As, which showed moderate pollution levels. The overall ecological risk in these areas was relatively low. The results of principal component analysis and correlation analysis indicated that Pb, Cu, and As were primarily sourced from human activities, while Cr was mainly of natural origin. Moreover, the distribution of heavy metals in the study areas was principally affected by TOC and salinity.