A key parameter in determining the exchange of CO2 across the ocean-atmosphere interface is the sea surface partial pressure of carbon dioxide (pCO2). Temperate seasonally stratified shelf seas represent a significant sink for atmospheric CO2. Here an analytical model is used to quantify the impact of vertical mixing across the seasonal thermocline on pCO2. The model includes the impacts of the resultant dissolved inorganic carbon, heat, salt, and alkalinity fluxes on the solubility of CO2 and the effect of the inorganic carbon sink created by the primary production fuelled by the flux of limiting nutrient. The results indicate that diapycnal mixing drives a modest but continuous change in pCO2 of order 1–10 µatm d−1. In quantifying the individual impacts of the fluxes of the different parameters, we find that the impact of the fluxes of DIC and nitrate fluxes dominate. In consequence, both the direction and magnitude of the change in pCO2 are strongly dependent on the C:N uptake ratio in primary production. While the smaller impacts of the heat and salt fluxes tend to compensate for each other at midshelf locations, the heat flux dominates close to the shelf break. The analysis highlights the importance of the accurate parameterization of the C:N uptake ratio, the surface-mixed layer depth, and the TKE dissipation rate within the seasonal thermocline in models to be used to predict the air-sea exchange of carbon dioxide in these regimes. The results implicate storms as key periods of pCO2 perturbation.