Blueberry (Vaccinium corymbosum L.) stands out among fruit in terms of three open physiological questions about its climacteric character, CO2 uptake, and the absence or presence of stomata on its floral organs. The objective of the present study was to examine the structures of blueberry flowers and fruit to explain their contribution to CO2 exchange and transpiration in order to clarify these discrepancies. Blueberries were dewaxed and the sepals/corolla removed for stomata counts, and their micromorphology was studied via LT-SEM. The fruit has stomata, contrary to beliefs in the literature, possibly because the stomata are occluded by the dense wax cover or ‘bloom’ and hidden on the distal part of the ovary in between and underneath the corolla. However, stomata were located on the distal part of the fruit surrounded by the sepals (calyx) and found predominantly on the abaxial sepals, while the adaxial side of the sepals and the proximal part of the ovary lacked stomata. The petals were devoid of stomata, trichomes, and chlorophyll and abscised after anthesis. In contrast, the sepals remained until maturity, contributing 5–7% to the berry surface but contributing to the majority of fruit stomata and chlorophyll. With 59–71% of the fruit’s chlorophyll, sepals were a significant source of the CO2 uptake. Similarly, with 95% of the berry stomata, sepals were a significant source of water loss, measured via porometry of fruit with and without sepals. Overall, this study identified the ovary as a minor source and sepals as the dominant source of CO2 and H2O exchange in blueberries.