Abstract The distributions of total carbon dioxide (TCO 2 ) and alkalinity (TA) in the upper layer at the SouthEast Asian Time-series Study (SEATS) station at 18°N, and 116°E in the northern South China Sea (SCS) were determined on 19 cruises between September 1999 and October 2003. The variations in the concentrations of TCO 2 and TA in the mixed layer, which ranged between 1860 and 1920 μmol kg −1 , and 2170 and 2230 μmol kg −1 , respectively, followed a distinct intra-annual pattern like that of salinity. The maximum concentrations were found in the winter as enhanced vertical mixing brought the subsurface Tropical Water, which was more saline and elevated in TA and TCO 2 , to the mixed layer. There was an even more well-defined and consistent intra-annual pattern in the variations in the associated fugacity of CO 2 , fCO 2 , that fluctuated between 340 and 400 μatm. However, the variations followed the temporal pattern in temperature more closely than that in salinity as fCO 2 rose systematically towards a maximum in the summer and then fell progressively to a minimum in the winter. The intra-annual variations in TA could be accounted for largely by the variations in salinity. Once TA was normalized to the average salinity of 33.5 in the mixed layer, the variations in the resulting NTA were only slightly larger than the analytical uncertainty and they did not follow a consistent intra-annual pattern. On the other hand, consistent intra-annual variations remained evident in NTCO 2 , TCO 2 normalized to a salinity of 33.5, and NfCO 2 , fCO 2 normalized to the average temperature of 27.6 °C in the mixed layer. In fact, the patterns in the intra-annual variations in NTCO 2 and NfCO 2 mimicked each other closely. From the late winter through the summer (February–August), the uptake of carbon in primary production and the evasion of CO 2 to the atmosphere led to a drawdown in NTCO 2 and a decrease in NfCO 2 . From the late summer to the early winter (August–December), variations in NTCO 2 and NfCO 2 were small. The variations in TCO 2 and fCO 2 could be explained largely by changes in salinity and temperature, respectively. In the winter (December–February), both NTCO 2 and NfCO 2 were at a maximum, indicating that the effects of the net invasion of atmospheric CO 2 to the SCS and the enhanced vertical mixing of the surface waters with the subsurface Tropical Water dominated over the effect from the higher primary production during this season. Atmospheric fCO 2 was less than fCO 2 in the mixed layer from April through October and exceeded the latter from November through March. For the year as a whole, there was a net invasion of CO 2 of 0.02 mol C m −2 yr −1 , a value that was indistinguishable from zero, indicating that the northern SCS was neither a significant source nor a significant sink of atmospheric CO 2 . Inter-annually, there were indications that NTCO 2 and fCO 2 in the mixed layer were increasing with time at rates of ∼1.5 μmol kg −1 yr −1 (or ∼0.1% yr −1 ) and ∼4 μatm yr −1 (or ∼1% yr −1 ), respectively between 1999 and 2003.