Smoo Cave is formed within Early Ordovician dolostones of the Durness Group (also known as the Durness Limestone). The cave has formed along the boundary between the light grey Sangomore Formation and the dark grey, mottled Sailmhor Formation (sometimes called Leopard Rock), both of which form part the Durness Group succession. These horizons close to the formation boundary are characterised by large and abundant chert nodules which can be found all along the inner stream chamber where they have been left behind after dissolution of the surrounding dolostone. The cave was formed along two geological lines of weakness by a combination of erosion from the sea and an inland underground stream which has formed the innermost chambers. Upstream of the Allt Smoo which runs into the cave, impermeable quartzites have been faulted against the Durness Limestone, causing the stream to sink down into the carbonate rock soon after it has crossed the contact between the two different rock types.