The RIVERSTRAHLER model, an idealized biogeochemical model of the river system, has been coupled to MIRO-CO2, a complex biogeochemical model describing diatom and Phaeocystis blooms and carbon and nutrient cycles in the marine domain, to assess the dual role of changing nutrient loads and increasing atmospheric CO2 as drivers of air–sea CO2 exchanges in the Southern North Sea with a focus on the Belgian coastal zone (BCZ). The whole area, submitted to the influence of two main rivers (Seine and Scheldt), is characterized by variable diatom and Phaeocystis colonies blooms which impact on the trophic status and air–sea CO2 fluxes of the coastal ecosystem. For this application, the MIRO-CO2 model is implemented in a 0D multibox frame covering the eutrophied Eastern English Channel and Southern North Sea and receiving loads from the rivers Seine and Scheldt. Model simulations are performed for the period between 1951 and 1998 using real forcing fields for sea surface temperature, wind speed and atmospheric CO2 and RIVERSTRAHLER simulations for river carbon and nutrient loads. Model results suggest that the BCZ shifted from a source of CO2 before 1970 (low eutrophication) towards a sink during the 1970–1990 period when anthropogenic DIN and P loads increased, stimulating C fixation by autotrophs. In agreement, a shift from net annual heterotrophy towards autotrophy in BCZ is simulated from 1980. The period after 1990 is characterized by a progressive decrease of P loads concomitant with a decrease of primary production and of the CO2 sink in the BCZ. At the end of the simulation period, the BCZ ecosystem is again net heterotroph and acts as a source of CO2 to the atmosphere. R-MIRO-CO2 scenarios testing the relative impact of temperature, wind speed, atmospheric CO2 and river loads variability on the simulated air–sea CO2 fluxes suggest that the trend in air–sea CO2 fluxes simulated between 1951 and 1998 in the BCZ was mainly controlled by the magnitude and the ratio of inorganic nutrient river loads. Quantitative nutrient changes control the level of primary production while qualitative changes modulate the relative contribution of diatoms and Phaeocystis to this flux and hence the sequestration of atmospheric CO2.