Thermodynamic calculations and inorganic precipitation experiments indicate a relationship between aragonite Mg/Ca and water temperature. This offers a route to reconstruct seawater temperatures from fossil corals. Fundamental to this is the assumption that Mg2+ exchanges for Ca2+ within carbonate. We present X-ray Absorption Fine Structure (XAFS) data to indicate the structural state of Mg in modern Porites coral skeletons. We show Mg is not in aragonite, but hosted by a disordered Mg-bearing material. Mg may be predominantly hosted in organic materials or as a highly disordered inorganic phase, e.g., a nanoparticulate form of Mg carbonate or hydroxide. Reported correlations between seawater temperature and coral Mg/Ca are unlikely to be consistent between corals and hence analysis of Mg/Ca in fossils is unlikely to produce accurate climate reconstructions. We anticipate XAFS will be applied widely to environmental proxies and become an important tool in identifying those that reconstruct accurate climates.