Seven sediment cores from the Palaea and Nea Kameni hydrothermal embayments (PK and NK) on Santorini have been studied by using sediment smear slides, X-ray diffraction, and radiocarbon techniques to determine their lithology, mineralogy, and age, respectively. The cores have been analyzed chemically for a suite of elements, including selective chemical leaching, to determine the partition of elements between coexisting phases. Lithologically and chemically, the sediments from the two embayments are very different. Sediments from PK are oxidized in the upper parts of the cores and reduced at depth; they comprise mainly hydrothermal pyritiferous diatomaceous ooze with minor Fe oxyhydroxide, volcanic debris, gypsum, and siderite. Sediments from NK are oxidized throughout and comprise predominantly amorphous iron oxyhydroxides and goethite; they are thought to have formed by direct precipitation from solution. In PK, biogenic, detrital seawater evaporate, and hydrothermal sediment phases have been identified but only the detrital inputs can be correlated between cores. Mn shows a pronounced enrichment towards the outer part of the embayment because of its dispersion down the embayment and precipitation in the more-oxidizing sediments towards the open sea. In NK, the sediments contain detrital, seawater evaporate, and hydrothermally precipitated and scavenged phases. The presence of substantial amounts of organic matter in the PK sediments but not in the NK sediments is probably the main reason why geochemical processes in the two embayments are different.