Deciphering the intensity and range of variation in fault-related rock composition defines the nature and timing of fluid-rock interactions within fault zones. We investigate the distribution, concentration, and nature of mineralogic and elemental transformations at numerous exhumed and cored sites on the active and ancient San Andreas fault system over a 0-5 km depth range with traditional mineral analyses, optical and scanning electron microscopy, whole-rock geochemistry, high-resolution X-Ray Fluorescence imaging, and X-Ray spectroscopy acquired at the SSRL synchrotron. Rocks in the cores of fault zones of the San Andreas System exhibit changes of Proterozoic and Cretaceous feldspar-hornblende-biotite-rich protoliths to clays, hydrous phyllosilicates, chloritic minerals, and carbonates. Likely Quaternary fault surfaces that formed at 5-10 m depth in poorly consolidated sedimentary deposits exhibit Fe-Mg-phyllosilicate-rich foliated cataclasites. Fault zones that developed at 100 m – to 4 km depth exhibit indurated rocks with carbonate-high temperature zeolite-epidote mineralization, ductile deformation, micro-fold-thrust structures in chlorites, rare pseudotachylyte, clay-clast aggregates, and injection veins. Micron-scale observations document Fe, Mg, Cr, Ti, Mn mobility in slip surfaces and into adjacent microfractures in the damage zones. X-Ray spectroscopy indicates that micron-scale reduction of Mn and Fe occurred, and in places, flow-like textures suggest fluidized metal movement in the fault zones. Adapting concepts from Kanamori and Lachenbruch types of analyses, we suggest that earthquakes provide thermal energy that drives the reactions and hydrothermal alteration. These reaction products can then be the loci of aseismic creep and may help explain how coseismic slip deficits develop in the upper parts of faults. The absence of 'clay gouge', incohesive fault rocks, and breccias, and the pervasiveness of evidence for syntectonic alteration suggest that revisions to canonical fault models could incorporate the complexity of fault composition and structure observed by many recent workers. This includes mm- to cm-thick cataclasite slip surfaces that accommodate the bulk of seismic slip to the Earth’s surface, embedded within cohesive, sheared, and damaged fault-related rocks to depths> 5 km.