The processes involved in vital effects, defined as biological processes overriding environmental signals, are not well understood and this hampers the interpretation of environmental parameters such as seawater temperature. Insufficient knowledge is available about changes in physico-chemical parameters, in particular those related to crystallography, associated with biomineral formation and emplacement. This paper assesses the influence of crystallography on Mg2+ concentration and distribution in calcite biominerals of bivalved marine organisms, mussels and rhynchonelliform brachiopods, and considers the implications for Mg/Ca thermometry. In the mussel Mytilus edulis, changes in Mg2+ are not associated with crystallography; but in the brachiopod Terebratulina retusa, increases in Mg2+ concentrations (∼0·5–0·6 wt. ) are associated with the {0001 planes of calcite biominerals. A comparison between mussels and brachiopods with avian eggshells, which form at constant ambient temperature, also reveals that there is at least a common 0·1 wt. variation in magnesium concentration in these calcite biomineral systems unrelated to temperature or crystallography. Results demonstrate that the integration of contextual crystallographic, biological and chemical information may be important to extract accurate environmental information from biominerals.