In this study, microstructural features of calcareous segments from the macro-alga species Halimeda opuntia are investigated using scanning electron microscopy. The intention was to study the algal segment´s calcium carbonate microstructure in detail, in order to be able to explain the formation of skeletal features in relation to known physiological processes of the alga. Furthermore, potential alteration of the Halimeda segment microstructure due to elevated seawater pCO2 and corresponding shifts in seawater carbon chemistry and calcium carbonate saturation are investigated. Laboratory experiments show that segment calcification is not impacted by seawater elevated in pCO2 and lower carbonate saturation state. However, the process of lifetime segment cementation is affected overall leading to a more acicular and fragile skeletal microstructure. Based on the microstructural investigations, a theoretical model is developed on how physiological daytime and nighttime processes may facilitate the formation of skeletal features in the algal genus Halimeda. The model aims to illustrate basic relationships between the physiology of the alga, the seawater carbon chemistry and the observed skeletal microstructure of the segment when seawater pCO2 is elevated.