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We examine deformed crystalline bedrock in the upper parts of the active San Andreas and ancient San Gabriel Faults, southern California, to 1) determine the nature and origin of micro-scale composition and geochemistry of fault-related rocks, 2) constrain the extent of fluid-rock interactions, and 3) determine the interactions between alteration, mineralization, and deformation. We used drill cores from a 470 m long inclined borehole through the steep-dipping San Gabriel Fault and from seven inclined northeast-plunging boreholes across the San Andreas Fault zone to 150 m deep to show that narrow fault cores 10 cm to 5 m wide lie within 100s m wide damage zones. Petrographic, mineralogic, whole-rock geochemical analyses and synchrotron-based X-ray fluorescence mapping of drill core and thin sections of rocks from the damage zone and narrow principal slip surfaces reveal evidence for the development of early fracture networks, with iron and other transition element mineralization and alteration along the fractures. Alteration includes clay $$\pm$$ chlorite development, carbonate, and zeolite mineralization in matrix and fractures and the mobility of trace and transition elements. Carbonate-zeolite mineralization filled fractures and are associated with element mobility through the crystalline rocks. Textural evidence for repeated shearing, alteration, vein formation, brittle deformation, fault slip, pressure solution, and faulted rock re-lithification indicates significant hydrothermal alteration occurred during shallow-level deformation in the fault zones. The rock assemblages show that hydrothermal conditions in active faults develop at very shallow levels where seismic energy, heat, and fluids are focused.