A geometrically well-defined sill, intruded into tuff, provides a paleoanalogue for assessing hydro-thermal-geochemical processes around a nuclear waste repository. Changes in the porosity and permeability of the tuff are attributable to hydrothermal alteration driven by heat from the sill. Precipitation of cristobalite and clinoptilolite in pores within 1 cm of fracture walls reduces vitric tuff porosity and permeability from 20% to 0% and from 10−14 m2 to 10−21 m2, respectively. Measured porosity changes near fracture walls fit a simple analytical model of silica migration via isothermal diffusion. In heated devitrified tuff, silica migration alters porosity and permeability by precipitation of quartz. Analogous hydrologic changes to the devitrified host rock around a hot nuclear waste repository will lead to increased amounts of water entering the repository via fracture flow.