Carbon dioxide concentrating mechanisms (CCMs) act to improve the supply of CO2 at the active site of ribulose-1,5-bisphosphate carboxylase/oxygenase. There is substantial evidence that in some microalgal species CCMs involve an external carbonic anhydrase (CAext) and that CAext activity is induced by low CO2 concentrations in the growth medium. However, much of this work has been conducted on cells adapted to air-equilibrium concentrations of CO2, rather than to changing CO2 conditions caused by growing microalgal populations. We investigated the role of CAext in inorganic carbon (Ci) acquisition and photosynthesis at three sampling points during the growth cycle of the cosmopolitan marine diatom Chaetoceros muelleri. We observed that CAext activity increased with decreasing Ci, particularly CO2, concentration, supporting the idea that CAext is modulated by external CO2 concentration. Additionally, we found that the contribution of CAext activity to carbon acquisition for photosynthesis varies over time, increasing between the first and second sampling points before decreasing at the last sampling point, where external pH was high. Lastly, decreases in maximum quantum yield of photosystem II (Fv/Fm), chlorophyll, maximum relative electron transport rate, light harvesting efficiency (α) and maximum rates of Ci- saturated photosynthesis (Vmax) were observed over time. Despite this decrease in photosynthetic capacity an up-regulation of CCM activity, indicated by a decreasing half-saturation constant for CO2 (K0.5CO2), occurred over time. The flexibility of the CCM during the course of growth in C. muelleri may contribute to the reported dominance and persistence of this species in phytoplankton blooms.