Shenandoah contains portions of the headwaters for three major watersheds in Virginia: the Rappahannock, the Shenandoah, and the James Rivers. Each of these rivers eventually flows into the Chesapeake Bay. The streams are formed from numerous springs, some of which are located near the ridge tops. The water from these springs is very cool and, on its downhill journey, forms the numerous high gradient and highly oxygenated streams found in the park. Due to the protection of the surrounding forests, the water in these streams is of high quality and low in sediment load.
As a result of high air pollution levels, atmospheric deposition in Shenandoah National Park is the greatest threat to the protected mountain streams. Acid precipitation, a type of atmospheric deposition that is primarily linked to fossil fuel combustion, is lowering water pH in some extremely sensitive streams both chronically and episodically. The low buffering capacity of a large percentage of soils in the park provides limited protection from acid depositions. Because of the sensitivity of the streams in the park to acidification, long-term monitoring of stream water chemistry and hydrogeochemical processes is a major component of the Inventory and Monitoring Program in the park.