AbstractCO₂ signatures differ among locations, even within the same coastal habitat. However, the driving mechanism behind this variation is not well understood due to the presence of both human and natural stresses. This study examines seawater pCO₂ and its deviation from the regional average (defined as pCO₂ anomaly) during spring, summer, and winter at two contrasting zones (trial and core zones) of Dongshan coral habitat. The impact of solar, tidal, and biological cycles on pCO₂ anomaly is relatively small under the designed sampling scheme. Results show that there is a large positive pCO₂ anomaly in the turbid water of the trial zone during all studied seasons, while the large negative pCO₂ anomaly in the core zone only occurs during the summer upwelling season. This indicates that CO₂ signatures among locations may have seasonality. The physical and biological contributors to pCO₂ anomaly are then quantitatively revealed based on a first‐order Taylor decomposition and biological carbon metabolisms. The results suggest that organic carbon metabolism of marine phytoplankton dominated pCO₂ anomaly in all three seasons, while inorganic carbon metabolism also enlarged pCO₂ anomaly, especially during summer. Physical contributions were minor. Moreover, significant linear correlations between turbidity (related to local human activities), chlorophyll (related to coastal upwelling) and changes in dissolved inorganic carbon (induced by organic carbon metabolism) indicate human and natural influences on bioprocesses, which may enhance pCO₂ anomaly. Finally, the Dongshan coral habitat was estimated as a source of atmospheric CO₂, with an annual efflux of approximately 50 t C.