To investigate the controls on the geochemistry of aragonitic sclerosponge skeletons, we used secondary ion mass spectrometry (SIMS) to analyse an Astrosclera willeyana specimen. The high spatial resolution of SIMS allows the independent analysis of the two key crystal structures in the skeleton i.e. the fused spherulites (formed intracellularly and fused together at the surface of the skeleton) and the epitaxial backfill (deposited extracellularly at the base of the sponge tissue). We analysed Sr/Ca, Mg/Ca and Ba/Ca across a short (~ 5 mm) transect of fused spherulites which represented several years growth. We observe cyclical variations (with a length of 0.1 to 0.6 mm in both Sr/Ca and Mg/Ca in some (but not all) sections of the transect. The observed ranges of Sr/Ca and Mg/Ca over the presumed seasonal cycles are ~ 9.5 to 11.5 mmol mol− 1 and 0.6 to 1.0 mmol mol− 1 respectively. The annual seawater temperature range at the study site is ~ 4.3 °C, so the inferred temperature sensitivity of skeletal Sr/Ca and Mg/Ca is ~ 0.5 mmol mol− 1 °C (or 5% °C− 1) and ~ 0.1 mmol mol− 1°C (or 13% °C− 1) respectively. This is higher than observed in most previous sclerosponge studies or anticipated from studies of synthetic aragonite. This indicates that the chemistry of the A. willeyana skeleton is affected by one or more additional influences, besides temperature, which are currently unresolved. The pH of the precipitating fluid, estimated from skeletal δ11B, is ~ 8.1–8.2 for both fused spherulites and epitaxial backfill. Epitaxial backfill contains significantly higher Sr/Ca, Mg/Ca and B/Ca and significantly lower Ba/Ca than the fused spherulites but Sr/Ca and Mg/Ca are positively correlated by the same relationship in both skeletal features. This suggests that the geochemistry of each feature is predominantly controlled by a common process. This is unlikely to be Rayleigh fractionation, which is indicated by negative correlations between Sr and Mg in aragonite.