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Human–environment interactions across historical periods in China have been well reconstructed over the past decade; however, few studies have focused on southern China, particularly Hainan Island. This study investigated two sediment cores (cores X1 and X2) collected from the continental shelf off Hainan Island in the northern South China Sea. Combined with geochemical compositions (Al, Ni, Cu, Zn, Cd, and Pb), Sr-Nd isotopes, grain size, and AMS 14C ages, our results showed that Cd and Cu in core X1 and Cd and Pb in core X2 have been mainly influenced by anthropogenic activities since ~4.0 kyr BP. The enrichment factors showed obvious increases starting at ~4.0 kyr BP and were in good accordance with the appearance of abundant archeological sites on Hainan Island. Significant climatic changes (i.e. decreases in the East Asian summer monsoon and increases in El Niño–Southern Oscillation activities) at ~4.0 kyr BP likely promoted more intense, localized human activities, which in turn enhanced heavy metal accumulation in the continental shelf sediments. These results provide new insights into the history of human activities on Hainan Island and indicate that the geochemical compositions of continental shelf sediments have the potential for broadening our knowledge of the human activities and cultural development in tropical areas. [ABSTRACT FROM AUTHOR]