The pyroclastic deposits of the Minoan eruption (ca 3600 yr bp) in Santorini contain abundant xenoliths. Most of these deposits are calcareous blocks of laminated-botryoidal, stromatolite-like buildups that formed in the shallow waters of the flooded pre-Minoan caldera; they consist of (i) light laminae, of fibrous aragonite arranged perpendicular to layering, and (ii) dark laminae, with calcified filaments of probable biological origin. These microstructures are absent in the light laminae, suggesting a predominant inorganic precipitation of aragonite on substrates probably colonized by microbes. Internal cavities contain loose skeletal grains (molluscs, ostracods, foraminifera and diatoms) that comprise taxa typical of shallow marine and/or lagoon environments. Most of these forms are typical of warm water environments, although no typical taxa from hydrothermal vents have been observed. Past gasohydrothermal venting is recorded by the occurrence of barite, pyrolusite and pyrite traces. The most striking features of the stable isotopic data set are: (i) an overall wide range in δ13CPDB (0·16 to 12·97‰) with a narrower variation for δ18OPDB (−0·23 to 4·33‰); and (ii) a relatively uniform isotopic composition for the fibrous aragonite (δ13C = 12·40 ± 0·43‰ and δ18O = 2·42 ± 0·77‰, n = 21). The δ13C and δ18O values from molluscs and ostracods display a covariant trend, which reflects a mixing between sea water and a fluid influenced by volcano-hydrothermal activity. Accordingly, 87Sr/86Sr from the studied carbonates (0·708758 to 0·709011 in fibrous aragonite and 0·708920 to 0·708991 in molluscs) suggests that the aragonite buildups developed in sea water under the influence of a hydrothermal/volcanic source. Significant differences in trace elements have been detected between the fibrous aragonite and modern marine aragonite cements. The caldera water from which the fibrous aragonite crusts formed received an input from a volcano-hydrothermal system, probably producing diffuse venting of volcanogenic CO2 gas and of a fluid enriched in Ca, Mn and Ba, and depleted in Mg and probably in Sr.