Deep Run Ponds Natural Area Preserve is a 907-acre protected area in Rockingham County, Virginia, preserving one of the state’s largest remaining systems of Shenandoah Valley sinkhole ponds. This distinctive landscape, also found in parts of Augusta County, is marked by pond water levels that rise and fall through the year. The preserve’s eight sinkhole ponds support a notable concentration of rare plant and animal life, including Virginia sneezeweed, black-fruited spikerush, northern St. John’s-wort, Buxbaum’s sedge, and northern bog clubmoss. Owned and maintained by the Virginia Department of Conservation and Recreation, the site is managed primarily as protected habitat, with no public access improvements and visits allowed only by prior arrangement.