The structure and stratigraphy of the Miocene formations east of San Francisco Bay have been described in multiple studies for over a century. We integrated the results of past investigations and provide new data that improve understanding of formation age, the timing of deformation, and the amount of dextral displacement on selected faults. New geologic mapping and better age control show that formations previously inferred to be separate units of different ages are correlative, and new names are proposed for these units. Miocene structures associated with the development of the San Andreas transform system exerted significant control on Miocene deposition in the East Bay area. The developing structure created five distinct stratigraphic sections that are differentiated on the basis of differences in the stratigraphic sequence, lithology, and age. The stratigraphic changes are attributed to significant dextral displacement, syndepositional faulting, and distal interfingering of sediment from tectonically elevated source areas. New stratigraphic evaluations and age control show that prior to ca. 6 Ma, the developing fault system created local tectonically induced uplift as well as spatially restricted subbasins. Regional folding did not occur until after 6 Ma. Past evaluations have inferred significant dextral displacement on some of the faults in the East Bay. The spatial relationships between unique conglomerate clasts and known source areas, as well as the distribution of well-dated and unique tuffs, suggest that dextral displacement on some faults in the East Bay is less than previously reported.