The vitric matrix of pre-caldera acid tuff and tuff breccia of the Santorini volcano, Aegean Sea, Greece has been generally replaced by one or more of the following authigenic minerals: K-rich and (K,Ca)-rich clinoptilolite, mordenite, opal-CT, and clay minerals. Halite is also present in some samples. Initial compositional inhomogeneities between the dacitic blocks in tuff breccia and tuff seem to have controlled the type of K-rich heulandite-group zeolite that formed. Mordenite postdates the heulandite-group zeolites and opal-CT. Some mordenite has replaced the rims of glass shards. The alteration minerals are not related to vertical or lateral zonation, and the irregular distribution of their assemblages is attributed to variations in heat flow, ionic activity in interstitial waters, and permeability. The pyroclastic rocks were in a region of active heat flow during and after their emplacement. The formation of authigenic silicates may have led to the sealing of open spaces and fractures, imposing barriers to permeability and subdividing the original open system into smaller closed systems. As alteration progressed, some of the trapped water in each individual domain was consumed in hydration reactions. Salts could have been concentrated by such a process, and halite probably precipitated from solutions of appropriate composition in the individual closed systems.