Tropical coral reef lagoons that are characterized by high deposition rates are potentially useful for high-resolution palaeoenvironmental reconstructions. We present the geochemical and accelerator mass spectrometry (AMS) 14 C-dating data of a 113-cm gravity core obtained from the Yongle atoll lagoon in the South China Sea. The core record preserves a continuous 1,500-year depositional history of the back-reef lagoon environment, with sedimentation rates varying from 0.55 to 1.55 mm yr −1 (mean of 0.74 mm yr −1 ). Calcium carbonate (CaCO 3 ) production was calculated based on the sediment accumulation rates and sediment density to be 807 g m −2 yr −1 . The geochemical records of the studied core displayed a progressively increasing trend of storms over the past 1,500 years. The stable carbon and oxygen isotopes of the lagoon sediment have the potential to record monsoon intensity. The lagoon system of the Yongle atoll appears to have been influenced by minor terrestrial input from 1,500 calendar years before present (cal yr BP) to 500 cal yr BP, and by a strong anthropogenic influence over the past 200 years.