During the periods of maximum cold in the Quaternary, major ice sheets covered Scotland. An ice stream hundreds of metres thick curved out from the Moray Firth to cross the plain of Caithness and flow over Orkney towards ice limits close to the edge of continental shelf. The great Scandinavian ice sheet probably lay to the east but there is no sure sign that it reached Orkney, although a few stones matched to Norwegian types were described in the 19th century. During the intervening warm interglacial periods the ice probably disappeared completely from Scotland. Long intervals of cool to cold conditions during the Quaternary saw the build up of mountain glaciers in Scotland and probably led to the episodic formation of small glaciers in the corries and valleys of Hoy.

NASA image of part of the Larsen ice shelf, Antarctica
The timing of glaciation on Orkney is unclear. Evidence from offshore indicates that the Ice Age started about 2.4 million years ago. The major ice sheets developed at intervals after 850,000 years ago, with the last (Devensian) ice sheet expanding after 32, 000 years ago. This ice eventually retreated and thinned, with its final disappearance from Orkney about 16,000 years ago.
The passage of ice sheets shaped the existing hills and ridges to give a pronounced SW-NE grain to the topography of Mainland and Rousay and excavated the sounds between the islands. The rocks embedded in the ice left scratch marks, known as striations, on the bedrock, giving the general direction of movement of the ice towards the northwest. The ice carried rocks from its source area in Scotland, including metamorphic erratics, and from the bed of the North Sea, including chalk and flint, but the bulk of the material is derived more locally from the Devonian sandstones. Much soft sediment was scraped up by the ice from what is now the sea bed and the resultant mix of mud, sand, broken shells and stones gives the layer of boulder clay that now covers much of Orkney in a blanket from a few centimetres to 20 metres deep. The best place to view this material is at Scara Taing, Rousay, where three distinct layers of boulder clay are superposed, each resting locally on a striated sandstone pavement. The final movement of the thinning ice sheet moulded the boulder clay of Harray and Rousay into a series of low, elongate hills or drumlins.
After a brief amelioration of climate, the short and suddenly cold period known as the Loch Lomond Stadial, 13,000 to 11,500 years ago, terminated the Devensian cold stage. A small glacier probably reformed in Enegars corrie on Hoy and conditions of arctic severity prevailed throughout Orkney. Permafrost gripped the ground, with frost shattering of barren rock surfaces and the churning and solifluction of boulder clay deposits. After 11,500 years and 10,500 years ago, the climate changed abruptly to warmer conditions than the present time and sea water levels rose rapidly.