Several caves in the Shenandoah Valley in Virginia show evidence for early hypogenic conduit development with later-enhanced solution under partly confined phreatic conditions guided by geologic structures. Many (but not all) of these caves have been subsequently invaded by surface waters as a result of erosion and exhumation. Those not so affected are relict phreatic caves, bearing no relation to modern drainage patterns. Field and petrographic evidence shows that carbonate rocks hosting certain relict phreatic caves were dolomitized and/or silicified by early hydrothermal fluid migration in zones that served to locally enhance rock porosity, thus providing preferential pathways for later solution by groundwater flow, and making the surrounding bedrock more resistant to surficial weathering to result in caves that reside within isolated hills on the land surface. Features suggesting that deep phreatic processes dominated the development of these relict caves include (1) cave passage morphologies indicative of ascending fluids, (2) cave plans of irregular pattern, reflecting early maze or anastomosing development, (3) a general lack of cave breakdown and cave streams or cave stream deposits, and (4) calcite wall and pool coatings within isolated caves intersecting the local water table, and within unroofed caves at topographic locations elevated well above the local base level. Episodes of deep karstification were likely separated by long periods of geologic time, encompassing multiple phases of sedimentary fill and excavation within caves, and reflect a complex history of deep fluid migration that set the stage for later shallow speleogenesis that continues today.