The paleoenvironmental history of the Beilun River estuary on the coast of Beibu Gulf in the northwest South China Sea is reconstructed based on fossil diatoms, isotopic dating, sedimentary grain size data, mineralogy and geochemistry in three sediment core samples. Results show that the estuary has experienced significant environmental changes since deposition began about 20,000 yr ago. Freshwater runoff of the Beilun River initially was strong. However, the freshwater runoff reduced significantly after a transgressive event. Subsequently the estuary’s position began to migrate to the northeast. At the end of the Late Pleistocene the estuary shifted gradually towards the southwest. In the Early-Mid Holocene, the estuary’s geomorphology was shaped by seawater transgressing into the ancient river channel. The basin was filled continuously but slowly to form the present Beilun River estuary. Holocene transgression in this area could be divided roughly into three stages, including oscillation period 1, the maximum transgression period, and oscillation period 2.