Deep Run Ponds Natural Area Preserve is a 706-acre (285.7 ha) Natural Area Preserve located in Rockingham County, Virginia. It contains one of the largest remaining systems of Shenandoah Valley sinkhole ponds in the Commonwealth. Such ponds are found in Rockingham and Augusta Counties; their water levels fluctuate throughout the year. They support a variety of rare plant and animal life. Eight sinkhole ponds are located within the preserve's boundaries; two support the rare Helenium virginicum, while others contain Eleocharis melanocarpa, Hypericum boreale, Carex buxbaumi, and Lycopodiella inundata.