<p>The Bay of Marseille (BoM, France) is impacted by the urbanized and industrialized Aix-Marseille Metropolis, which is subject to significant increases in anthropogenic emissions of CO<sub>2</sub>. A carbonate chemistry balance module has been implemented into a biogeochemical model of the planktonic food web. The resulting model, named Eco3M-CarbOx includes 22 states variables that are dispatched into 5 compartments: phytoplankton, heterotrophic bacteria, detritus, dissolved organic and inorganic matter. The model suggests that the variability of the dissolved inorganic carbon system is mainly driven by the seawater temperature dynamics. A seasonal trend is identified by the model and it shows that, during the mixed water column period, the BoM is a sink for atmospheric CO<sub>2</sub> and a net autotroph ecosystem, while during stratified water column period, the BoM is a source of CO<sub>2</sub> to the atmosphere and a net heterotroph ecosystem. External forcings have an important impact on the carbonate equilibrium. Wind events change seawater temperature quickly, as during upwelling, for which the BoM waters change within a few days from a source of CO<sub>2</sub> to the atmosphere to a sink into the ocean. Moreover, the higher the wind speed is, the higher the air-sea CO<sub>2</sub> gas exchange fluxes are. The river intrusions with nitrate and alkalinity supplies lead to a decrease in the <i>p</i>CO<sub>2</sub> value, favoring the conditions of a sink of atmospheric CO<sub>2</sub> into the BoM. The nearby highly urbanized environment of the Aix-Marseille metropolis produces strong atmospheric values of CO<sub>2</sub>, also favoring the conditions of a sink of atmospheric CO<sub>2</sub> into the waters of the BoM.</p>