The Harpers Ferry quadrangle covers a portion of the northeast-plunging Blue Ridge-South Mountain anticlinorium, a west-verging allochthonous fold complex of the late Paleozoic Alleghanian orogeny. The core of the anticlinorium consists of high-grade paragneisses and granitic gneisses that are related to the Grenville orogeny. These rocks are intruded by Late Proterozoic metadiabase and metarhyolite dikes and are unconformably overlain by Late Proterozoic metasedimentary rocks of the Swift Run Formation and metavolcanic rocks of the Catoctin Formation, which accumulated during continental rifting of Laurentia (native North America) that resulted in the opening of the Iapetus Ocean. Lower Cambrian metasedimentary rocks of the Loudoun, Weverton, Harpers, and Antietam Formations and carbonate rocks of the Tomstown Formation were deposited in the rift-to-drift transition as the early Paleozoic passive continental margin evolved.
The Short Hill fault is an early Paleozoic normal fault that was contractionally reactivated as a thrust fault and folded in the late Paleozoic. The Keedysville detachment is a folded thrust fault at the contact of the Antietam and Tomstown Formations. Late Paleozoic shear zones and thrust faults are common.
These rocks were deformed and metamorphosed to greenschist-facies during the formation of the anticlinorium. The Alleghanian deformation was accompanied by a main fold phase and a regional penetrative axial plane cleavage, which was followed by a minor fold phase with crenulation cleavage. Early Jurassic diabase dikes transected the anticlinorium during Mesozoic continental rifting that resulted in the opening of the Atlantic Ocean. Cenozoic deposits that overlie the bedrock include bedrock landslides, terraces, colluvium, and alluvium.