We have analyzed core MD01-2392, ∽360 km east of the Mekong River mouth in the South China Sea (SCS). Over the past 500 ka, planktonic foraminiferal oxygen-isotopic values are consistently lighter than northern SCS and open-ocean records by up to 0.5‰, indicating the influence of run-off from the Mekong River during both glacial and interglacial periods. Carbonate content is higher during interglacials; sedimentation rates were higher during glacials. Increased sedimentation rates since 30 ka imply increased run-off during the last glacial maximum and Holocene Period. Contrary to general experience, in which it is classed as a warm species for temperature estimates, the thermocline-dwelling species Pulleniatina obliquiloculata increased its numbers during glacial periods. This implies an estuarine circulation and even brackish-water caps during glacial periods, reinforcing the sense of strong run-off. In an overall decline of warm water, the thermocline shoaled stepwise, with rapid rises across the glacial terminations. We infer that the southern SCS was opened to an influx of Indian Ocean waters through southern passages at those times of rising sea levels.