The contribution of coastal oceans to the global air-sea CO₂ flux is poorly quantified due to insufficient availability of observations and inherent variability of physical, biological and chemical processes. We present simulated air-sea CO₂ fluxes from a high-resolution biogeochemical model for the North American east coast continental shelves, a region characterized by significant sediment denitrification. Decreased availability of fixed nitrogen due to denitrification reduces primary production and incorporation of inorganic carbon into organic matter, which leads to an increase in seawater pCO₂, but also increases alkalinity, which leads to an opposing decrease in seawater pCO₂. Comparison of simulations with different numerical treatments of denitrification and alkalinity allow us to separate and quantify the contributions of sediment denitrification to air-sea CO₂ flux. The effective alkalinity flux resulting from denitrification is large compared to estimates of anthropogenically driven coastal acidification.