We estimated carbon and water flows, canopy conductance and the assimilation/transpiration ratio of fruiting and non-fruiting apple trees grown in the field, from daily gas exchange measurements taken during the summer with a whole-canopy enclosure device. The relationships between photosynthetic and transpirational responses and environmental conditions were also investigated, as well as the role of canopy conductance in controlling carbon dioxide and water vapor exchange. Light-saturated net photosynthetic rates, which were higher for the fruiting canopy than for the non-fruiting canopy, showed a general decrease in the afternoon, particularly for the non-fruiting canopy, compared with rates in the morning. When light was not limiting, the afternoon decrease in net photosynthesis appeared to be regulated more by non-stomatal factors than by changes in canopy conductance. Canopy conductance, which was higher for the fruiting canopy than for the non-fruiting canopy, may actively regulate photosynthetic activity and may also be modulated by feedback control in response to assimilation capacity. We conclude that adjustments in canopy conductance, which were partially dependent on the vegetative-reproductive status of the tree, control the equilibrium between photosynthesis and transpiration. We also demonstrated that whole-canopy chambers can be used to estimate photosynthetic and transpirational responses thereby overcoming the difficulty of scaling these physiological responses from the leaf to the whole-canopy level.