Diatoms are responsible for a large fraction of CO(2) export to deep seawater, a process responsible for low modern-day CO(2) concentrations in surface seawater and the atmosphere. Like other photosynthetic organisms, diatoms have adapted to these low ambient concentrations by operating a CO(2) concentrating mechanism (CCM) to elevate the concentration of CO(2) at the site of fixation. We used mass spectrometric measurements of passive and active cellular carbon fluxes and model simulations of these fluxes to better understand the stoichiometric and energetic efficiency and the physiological architecture of the diatom CCM. The membranes of diatoms are highly permeable to CO(2), resulting in a large diffusive exchange of CO(2) between the cell and external milieu. An active transport of carbon from the cytoplasm into the chloroplast is the main driver of the diatom CCM. Only one-third of this carbon flux is fixed photosynthetically, and the rest is lost by CO(2) diffusion back to the cytoplasm. Both the passive influx of CO(2) from the external medium and the recycling of the CO(2) leaking out of the chloroplast are achieved by the activity of a carbonic anhydrase enzyme combined with the maintenance of a low concentration of HCO(3)(-) in the cytoplasm. To achieve the CO(2) concentration necessary to saturate carbon fixation, the CO(2) is most likely concentrated within the pyrenoid, an organelle within the chloroplast where the CO(2)-fixating enzyme is located.