Living systems exert exquisite control on all aspects of biomineral production and organic components, including proteins, are essential to this biological control. The protein-rich extrapallial (EP) fluid of bivalve molluscs is a strong candidate for the source of such proteins. Differences in calcium carbonate polymorphs between Modiolus modiolus and Mytilus edulis are concurrent with differences in EP fluid protein profiles. In conjunction with this biological control is the environmental influence which is interpreted using proxies such as δ18O to determine the history of ambient seawater temperature. In the horse mussel, Modiolus modiolus, the difference in oxygen isotope fractionation in the nacreous aragonite and the prismatic aragonite layer results in respective δ18O values of 2.1±0.2% and 2.5±0.2%. These δ18O values result in estimates of ambient seawater of 12.1±0.6°C and 10.2±0.6°C for nacreous and prismatic aragonite, respectively. Electron backscatter diffraction is used here to determine the crystallographic orientation at high spatial resolution, allowing the measurements of stable isotopes to be accurately mapped in terms of shell architecture. These preliminary data suggest that it is essential to account for both polymorph and crystal habit when deciphering ambient seawater temperature using δ18O as a proxy.