Six coastal sediment cores collected from the northern South China Sea were dated by 210Pb and analyzed for stable carbon and oxygen isotope composition of planktonic foraminifer Globigerinoides ruber (δ13CGr and δ18OGr). Three of these cores were located east of Hainan Island and the other three off the Pearl River Estuary (PRE). Surface seawater δ18O and dissolved inorganic carbon (DIC) δ13C were identified as the dominant factors controlling downcore variations of δ18OGr and δ13CGr, respectively. Results of δ13CGr were then used to study surface water δ13CDIC and its relation to δ13C of atmospheric CO2 (δ13Catm) over the past century. Downcore records showed rather constant δ13CGr in cores off Hainan Island, but moderate decreases of δ13CGr, at rates between −0.006‰ and −0.009‰ per year, in cores off the PRE. Isotopic disequilibrium between δ13CDIC and δ13Catm was observed, with δ13CDIC apparently higher than expected at equilibrium with δ13Catm except at the site closest to the PRE. The relatively steady δ13CGr values east of Hainan Island were explained by balanced vertical mixing and biological pump, whereas the moderate δ13CGr decreases with time off the PRE were attributable to fluvial input of terrestrial carbon.