The experiments and simulations reported in this paper show that, for stomata sensitive to both CO2 and water vapour concentrations, responses of stomatal conductance (gws) to boundary layer thickness have two components, one resulting from changes in intercellular CO2 concentration (χci) and another from changes in leaf surface water vapour saturation deficit (Dws). The experiments and simulations also show that the boundary layer conductance (gwb) can significantly alter the apparent response of gws to ambient air CO2 mole fraction (χca) and water vapour mole fraction (χwa). Because of the feedback loop involved the responses of gws for χca and χwa each include responses to both χci and Dws. The boundary layer alters the state of the variables sensed by the guard cells—i.e. χci and Dws—and so it is a source of feedback. Thus, when scaling up from responses of stomata to the response of gws for a whole leaf, the effect of the boundary layer must be considered. The results indicate that, for given responses of gws to χci and Dws, the apparent responses of gws to Dwa and χca depend on the size of the leaf and wind speed, showing that this effect of the boundary layer should be considered when comparing data measured under different conditions, or with different methods.