Abstract. The equatorial Pacific Ocean is responsible for the interannual variability of the global ocean-atmosphere CO₂ fluxes. However, most ocean carbon models significantly underestimate the interannual variability of the regional ocean-atmosphere CO₂ fluxes. A basin-scale ocean circulation-biogeochemistry model is employed to investigate the uncertainties associated with the choice of gas exchange formulation, and to assess the implications of the choice of ecosystem model. Using four different, quadratic and cubic relationships of the gas transfer velocity with wind speed yields small differences in the integrated sea-to-air CO₂ flux (0.32 to 0.42 Pg C yr⁻¹), but large differences in the averaged Δ pCO₂ (44 to 73 μatm) for the area of 150° E–90° W, 10° N–10° S. While the choice of gas exchange formulation primarily influences the magnitudes, the choice of ecosystem model has a broader influence on the spatial and temporal variations in modeled carbon fields in the equatorial Pacific Ocean. Particularly, employing an ecosystem model without a dissolved organic pool overestimates the interannual variability in net community production, leading to under-estimated interannual variability of the basin-scale sea-to-air CO₂ flux.