Mapping of carbonate dissolution in nodular chert-bearing strata indicates that nodular chert formation in a diverse suite of Phanerozoic limestones occurred in bulk pore waters that were at calcite saturation. Opal-CT and quartz supersaturation was achieved in most chert-bearing strata by the intraformational dissolution of amorphous silica skeletal material. Chertification occurred by a combination of force of crystallization-controlled replacement of the host carbonate, whereby non-hydrostatic stresses resulting from opal-CT and quartz crystal growth caused calcite dissolution, and the isomineralic heterogenous nucleation of new opal-CT and quartz crystal at nodule peripheries. The restriction of the solution phase at silica-carbonate contacts to thin films permitted the preservation of ghosts of micron-sized features in the chert. Heterogeneities in sediment organic matter content, porosity, and biogenic silica concentrations promote the nucleation of chert nodules in some formations.