This came about at the end of the last ice age, when the moraine left by the retreating glacier blocked the original course of the River Swale on the west side of the fell and diverted it to its present course, forming a gorge to the east and leaving Kisdon isolated from other high ground.

One of these is the Pennine Way between the hamlets of Thwaite and Keld, which reaches a height of 420 metres on the eastern shoulder of the fell; while the bridleway between Keld and Muker, also known as the Old Corpse Road because it was formerly used as a corpse road to transport bodies for burial in consecrated ground lower down the valley, crosses the fell on the western side at a height of 470 metres.

100 metres east of the summit is a five-metre-deep shake hole, which is marked on the Ordnance Survey map as a pothole, so the depression may go much deeper on closer investigation.

The SSSI takes the form of four grazed enclosures with the combination of Calcareous grassland growing on limestone rock supporting exceptional and varied botanical species.

Other species include Sesleria albicans (blue moor grass), Carex pulicaris (flea sedge), Galium sterneri (limestone bedstraw), Orchis mascula (early purple orchid) and Primula vulgaris (primrose).