The Upper Cretaceous Williams Formation is the oldest unit within the San Onofre Mountains. It consists of sediment derived from exhumed plutonic and metavolcanic rocks of the Peninsular Ranges batholith. A locally preserved paleosol of probable Paleocene age indicates subaerial exposure of Cretaceous rocks. The Williams Formation is overlain disconformably by the Middle Eocene Santiago Formation. Three mappable members of the Santiago Formation were recognized on the basis of lithology and bedding characteristics. The lower, middle, and upper members represent an overall transgressive sequence of nonmarine to estuarine to shallow marine sandstone, siltstone, and mudstone. The Middle Miocene San Onofre Breccia, deposited unconformably on the Santiago Formation, marks an abrupt transition to debris flow and alluvial deposits. The San Onofre Breccia is composed of clasts of metamorphic rocks resembling Catalina schist, as well as pervasively fractured slide blocks of Catalina schist up to 0.7 mile in length. A transgressive marine sequence of sandstone, siltstone and siliceous shale of the Middle to Upper Miocene Monterey Formation overlies the San Onofre Breccia on the southwest flank of the San Onofre Mountains. A shallow marine environment persisted locally into the Pliocene, as indicated by coarse marine sandstone of the San Mateo Member of the Capistrano Formation. Uplift and emergence of the San Onofre Mountains during the Pleistocene left a series of marine terrace platforms incised into the seaward slope of the range.
The San Onofre Mountains contain several faults of limited strike length that are dominantly northwest- and northeast-trending. Normal faulting is the dominant fault style; however, several strike-slip faults were also recognized.