The mechanisms driving the air–sea exchange of carbon dioxide (CO2) in the North Sea are investigated using the three-dimensional coupled physical–biogeochemical model ECOHAM (ECOlogical-model, HAMburg). We validate our simulations using field data for the years 2001–2002 and identify the controls of the air–sea CO2 flux for two locations representative for the North Sea's biogeochemical provinces. In the seasonally stratified northern region, net CO2 uptake is high (2.06molm-2a-1) due to high net community production (NCP) in the surface water. Overflow production releasing semi-labile dissolved organic carbon needs to be considered for a realistic simulation of the low dissolved inorganic carbon (DIC) concentrations observed during summer. This biologically driven carbon drawdown outcompetes the temperature-driven rise in CO2 partial pressure (pCO2) during the productive season. In contrast, the permanently mixed southern region is a weak net CO2 source (0.78molm-2a-1). NCP is generally low except for the spring bloom because remineralization parallels primary production. Here, the pCO2 appears to be controlled by temperature.