Coastal areas are regions of active interaction between the sea and land and are highly sensitive to changes in heavy metal contamination caused by natural and anthropogenic activities. The contents of heavy metals in 80 surface sediments in the Qizhou Island sea area in the northeast of Hainan Island were determined to assess the contamination status, spatial distribution, sources, and ecological risks. The results indicate that the main factors influencing the distribution patterns and contents of heavy metals are hydrodynamic conditions and sources of materials. The accumulation of Cd and Pb in the sediments is attributed to the combined effects of natural sources and anthropogenic input. In addition to widespread anthropogenic influence, the enrichment of Cd in the southeastern outer shelf area of the study region may be controlled by biogenic carbonate rocks or enhanced input of near-source materials during the late Pleistocene low sea level period.