In this study, we investigated the seawater carbonate chemistry in the Dongsha Atoll Lagoon (DAL) in summer 2015, summer 2016, and autumn 2016. According to the calculation of the total alkalinity anomaly (ΔTA), the DAL is currently maintaining a net calcification status, with higher calcification potential in summer and lower calcification potential in autumn. The calculation of the partial pressure of CO2 anomaly (ΔpCO2) shows that the DAL acts as a CO2 source for the atmosphere, with higher ΔpCO2 values in summer and lower values in autumn. In addition to seasonal variation, ΔpCO2 also exhibits a clear variation between two summer investigations, with higher values in summer 2016 than in summer 2015, which could be associated with the different weather conditions during the sampling periods (2015 vs. 2016: sunny vs. stormy). Moreover, analyzing the salinity-normalized total alkalinity vs. dissolved inorganic carbon relationship reveals that calcification was the dominant process controlling the CO2 dynamics in summer 2015, while those in summer 2016 were regulated mainly by the combination of calcification and organic respiration. This result further suggests that the change in the organic carbon metabolism induced by the different weather conditions could be the driving force behind the observed variation in pCO2 between summer 2015 and 2016.