Abstract. We used micro-X-ray fluorescence combined with X-ray photoabsorption spectroscopy to investigate speciation-specific sulfur profiles in the inner shell layer of a giant clam (Hippopus hippopus). The sulfate, S-bearing amino acids, and total sulfur profiles indicated that inorganic sulfate was the dominant component in the shell of this bivalve. Sulfur profiles in the inner shell layer showed clear annual fluctuations that varied by more than one order of magnitude, from < 50 to 1420 ppm, and sulfate and total sulfur maxima became higher with age, whereas no ontogenetic trend was noticeable in the profile of S-bearing amino acids. A change in the carbonate ion concentration in the calcifying fluid would suggest that an ontogenetic increase in the relative activity of sulfate ions to carbonate ions in the calcifying fluid affects sulfate concentrations in the shells. These results suggest that trace sulfur profiles in the shell of the giant clam may reflect both cyclic shell growth related to environmental factors such as insolation and temperature and ontogenetic changes of the calcifying fluid chemistry mediated by physiological processes. The observed S profile implies a clear change in calcifying fluid chemistry towards less alkaline condition with age. Magnesium fluctuations suggested that Mg was incorporated into the shells at high growth rates during warm seasons. The spectrum of Mg K-edge X-ray absorption near edge structure (XANES) and comparison of Mg and S-bearing amino acids profiles indicated that a pronounced effect of the organic fraction or disordered phases were observed in aragonitic shell of H. hippopus rather than regulated substitution into the aragonite crystal lattice.