The Deep Run Ponds Natural Area Preserve in Rockingham County is one of the largest remaining Shenandoah Valley sinkhole pond systems in Virginia. Shenandoah Valley sinkhole ponds are found along the base of the Blue Ridge Mountains in Augusta and Rockingham Counties and are characterized by fluctuating water levels throughout the year. These sinkhole ponds comprise one of Virginia's most unusual and conservation-worthy ecosystems and support an interesting assemblage of rare plants and animals. This 668-acre natural area preserve includes eight sinkhole ponds, two of which support the globally rare Virginia sneezeweed (Helenium virginicum). Other rare species here include the Black-fruited spikerush (Eleocharis melanocarpa), Northern St. John's-wort (Hypericum boreale), Buxbaum's sedge (Carex buxbaumii) and Northern bog clubmoss (Lycopodiella inundata).
This recently acquired preserve has no public access facilities.