The Shenandoah Valley is a karst area, which means that slightly acidic water has worn away limestone and dolomite bedrock, over immense geological time producing caverns (of often spectacular shape and structure), underground waterways, streams and springs. Streams disappear and reappear, as do springs over time, and most of them communicate, either as recipients or contributors or both, with the Shenandoah River's two branches. Massanutten Mountain, the major visual landmark of the Valley, is elongated on a more or less north-south axis. It is traced on each side -- with a striking necklace-like elegance when viewed from the above -- by the wavering ribbons of the North and South forks of the Shenandoah. [image: courtesy of NASA] This 80-mile long suspended "necklace," stretching from Winchester on the north, to beyond Staunton on the south, defines the heart of the Shenandoah Watershed and indicates most but not all of the the surface area of what is known as the "geological Shenandoah" (there is also the "cultural Shenandoah" which extends down another 80 miles to Roanoke, VA). The Watershed is also the location of the seven major cavern systems which are an effect of the karstification of the Valley floor. In effect the entire area is a circulatory network of subterranean waterways of which the Shenandoah River is the dominant visible arterial support.

Wikipedia:

"The karstification of a landscape may result in a variety of large or small scale features both on the surface and beneath. On exposed surfaces, small features may include flutes, runnels, clints and grikes, collectively called karren or lapiez. Medium-sized surface features may include sinkholes or cenotes (closed basins), vertical shafts, foibe (inverted funnel shaped sinkholes), disappearing streams, and reappearing springs. Large-scale features may include limestone pavements, poljes and blind valleys. Mature karst landscapes, where more bedrock has been removed than remains, may result in karst towers or haystack/eggbox landscapes. Beneath the surface, complex underground drainage systems (such as karst aquifers) and extensive caves and cavern systems may form." 

U.S. Geological Survey: 

"Karst is a terrain with distinctive landforms and hydrology created from the dissolution of soluble rocks, principally limestone and dolomite. Karst terrain is characterized by springs, caves, sinkholes, and a unique hydrogeology that results in aquifers that are highly productive but extremely vulnerable to contamination. In the United States, about 40% of the ground water used for drinking comes from karst aquifers."

Further Reference sources:

Glossary of Karst terminology ("Virtual Karst")

The US Geological Survey ("USGS") Karst website