The shells of two marine bivalve species (Fulvia tenuicostata and Soletellina biradiata) endemic to south Western Australia have been characterised using a combined crystallographic, spectroscopic and geochemical approach. Both species have been described previously as purely aragonitic; however, this study identified the presence of three phases, namely aragonite, calcite and Mg-calcite, using XRD analysis. Data obtained via confocal Raman spectroscopy, electron probe microanalysis and laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) show correlations between Mg • S and Mg • P in F. tenuicostata and between Sr • S and S • Ba in S. biradiata. The composition of the organic macromolecules that constitute the shell organic matrix (i.e. the soluble phosphorus-dominated and/or insoluble sulfur-dominated fraction) influences the incorporation of Mg, Sr and Ba into the crystal lattice. Ionic substitution, particularly Ca2+ by Mg2+ in calcite in F. tenuicostata, appears to have been promoted by the combination of both S- and P-dominated organic macromolecules. The elemental composition of these two marine bivalve shells is species specific and influenced by many factors, such as crystallographic structure, organic macromolecule composition and environmental setting. In order to reliably use bivalve shells as proxies for paleoenvironmental reconstructions, both the organic and inorganic crystalline material need to be characterised to account for all influencing factors and accurately describe the "vital effect".