In situ field investigations coupled with coral culture experiments were carried out in the coral reef waters of the eastern coast of Shenzhen, Da’ao Bay (DAB), Dalu Bay (DLB), and Yangmeikeng Sea Area (YMKSA) to study the dynamics of the carbon dioxide (CO2) system in seawater and its controlling factors. The results indicated that the CO2 parameters were highly variable over a range of spatiotemporal scales, forced by various physical and biochemical processes. Comprehensively, DAB acted as a sink for atmospheric CO2 with exchange flux of –1.51 ± 0.31 to 0.27 ± 0.50 mmol C m−2 d−1, while DLB and YMKSA acted as a CO2 source with exchange fluxes of –0.42 ± 0.36 to 1.69 ± 0.74 mmol C m−2 d−1 and –0.58 ± 0.48 to 1.69 ± 0.41 mmol C m−2 d−1, respectively. The biological process and mixing effect could be the most important factor for the seasonal variation in total alkalinity (TA). In terms of dissolved inorganic carbon (DIC), in addition to biological process and mixing, its seasonal variation was affected by air–sea exchange and coral metabolism to some extent. Different from the former, the other CO2 parameters, total scale pH (pHT), partial pressure of CO2 (pCO2), and aragonite saturation state (ΩA), were mainly controlled by a combination of the temperature change, biochemical processes, air–sea exchange, and coral metabolism, while water mixing has little effect on them. In addition, our results indicated that coral communities could significantly increase the DIC/TA ratio by reducing the TA concentration and increasing the DIC in the reef waters, which may promote the acidification of local seawater and need attention.