Stony Creek originates in the George Washington National Forest and flows northward through Shenandoah County, Virginia, eventually joining the North Fork Shenandoah River near Edinburg. This freestone stream cuts through limestone and shale formations characteristic of the Valley and Ridge physiographic province, creating a mix of riffles, pools, and small rapids as it descends from the mountains.

The creek offers approximately 15.5 miles of paddleable water from Liberty Furnace downstream to its confluence with the North Fork Shenandoah River. This section has been classified as Class I-III whitewater, making it suitable for intermediate paddlers with some moving water experience. The upper reaches near Liberty Furnace provide more technical challenges, while lower sections become progressively calmer as the creek approaches the North Fork. Paddling opportunities are best from late fall through late spring when water levels are sufficient.

The creek is stocked with trout by the Virginia Department of Wildlife Resources eight times annually between October and May, as summer temperatures become too warm for trout survival. This stocking schedule coincides with optimal paddling conditions, though paddlers should be aware of anglers during these months.

The watershed supports a healthy riparian ecosystem with American holly, rhododendron, and wildflowers lining the banks. The creek provides habitat for both stocked rainbow trout and native brook trout in its tributaries. The endangered Candy Darter, considered one of North America's most colorful freshwater fish, inhabits these waters.

Access points include the area near Liberty Furnace in the upper section and various locations downstream toward Edinburg. The creek flows past Columbia Furnace, a historic iron-making site that operated in the 19th century. Big Stony Creek Road (Route 635) parallels much of the creek, providing road access to multiple put-in and take-out locations.

Harry Murray's Fly Shop in Edinburg serves as a local resource for creek conditions and is recognized as the oldest fly shop in Virginia. The shop holds the only permit to guide on small streams within Shenandoah National Park and provides expertise on Stony Creek fishing and paddling conditions.

Paddlers should note that water levels fluctuate significantly with rainfall, and the creek can become too low for navigation during dry periods or too dangerous during high water. The rocky streambed requires attention to avoid obstacles, and the relatively small size of the creek means that fallen trees and debris can create hazards that change seasonally.