The presence of vertical temperature and salinity gradients in the upper ocean and the occurrence of variations in temperature and salinity on time scales from hours to many years complicate the calculation of the flux of carbon dioxide (CO2) across the sea surface. Temperature and salinity affect the interfacial concentration of aqueous CO2 primarily through their effect on solubility with lesser effects related to saturated vapour pressure and the relationship between fugacity and partial pressure. The effects of temperature and salinity profiles in the water column and changes in the aqueous concentration act primarily through the partitioning of the carbonate system. Climatological calculations of flux require attention to variability in the upper ocean and to the limited validity of assuming “constant chemistry” in transforming measurements to climatological values. Contrary to some recent analysis, it is shown that the effect on CO2 fluxes of a cool skin on the sea surface is large and ubiquitous. An opposing effect on calculated fluxes is related to the occurrence of warm layers near the surface; this effect can be locally large but will usually coincide with periods of low exchange. A salty skin and salinity anomalies in the upper ocean also affect CO2 flux calculations, though these haline effects are generally weaker than the thermal effects. This article is protected by copyright. All rights reserved.