The storm was faced less by soldiers, and more by the sailors of the Allied navies in the Channel. The storm began as the result of two weather movements; the movement of a cold front over the British Isles southward from Iceland, and the movement of a warm front northward over France from the Mediterranean. This produced the conditions needed for a strong wind from the north-east, blowing down the Channel. June 18th 1944 started as a warm, calm day, but this was deceptive. The wind strengthened overnight, with a dramatic increase at about 3:30 on the 19th. By daybreak, the wind had strengthened to force 6 on the Beaufort Scale (21-26 knots, or 39-49 km/h), with gusts as high as force 8 (34-40 knots, or 62–74 km/h). Waves reaching 6-8 feet were present, even in the sheltered anchorages of the Mulberry harbours. There were hopes that the storm would not continue, as Channel storms were typically short things. These hopes were dashed overnight, as the wind continued throughout the 20th and 21st, strengthening as it did so. Waves of up to 15 feet in height were reported. Gale-force winds continued through the 22nd, but towards the evening, the wind dropped, and the sky cleared. The storm was over. It was not an especially strong storm by the standards of the North Atlantic, but its duration was unusual for the Channel. The direction of the wind, pushing the ships directly onto the beaches, did not help either.

The storm had a considerable effect on shipping in the Channel, and on the ships and landing craft unloading over the beaches. The ships and small craft were forced to seek shelter where they could. Unloading was cancelled, with crews being more preoccupied by their desperate fight for survival. The main shelters for the landing craft were the two Mulberry Harbours - artificial harbours constructed from concrete pontoons and steel breakwaters. One, administered by the Americans, was positioned off Saint-Laurent-sur-Mer, on Omaha Beach. The other, administered by the British, was at Arromanches, on Gold Beach. The 'Gooseberries', old ships sunk as breakwaters off each of the landing beaches, were also invaluable for protecting shipping during the gale. The American Mulberry was incomplete when the storm began; many of the concrete caissons (codenamed 'Phoenixes') were uncovered, allowing waves to break over and inside them, subjecting them to stresses they were not designed to hold off. Ships inside were thrown against them violently, hammering away at the concrete. Many cracked and broke apart, removing one important part of the breakwater. The commander of a British landing craft described the scene inside the harbour:

The scene inside the Mulberry was one of unutterable chaos. Literally hundreds of landing craft from LCV (Landing Craft Vehicle) to LST (Landing Ship Tank) were ashore, piled one upon another. The Whales (floating roadways) had vanished. The Bombardons (floating breakwaters) were chasing one another madly around the bay. The Phoenixes had cracked. Even the blockships were breaking up and what little searoom remained was packed with wreckage.

The British Mulberry fared better. It had more breakwaters in place, fewer ships inside, received protection from the waves thanks to the nearby Calvados Rocks, and was lying in shallower water. Even so, five of the Phoenix caissons were destroyed, the Bombardons broke away from the rest of the harbour and were carried out into the Channel, and several ships were driven ashore or capsized. Life in the less-sheltered Gooseberries was equally stressful and chaotic. Another British officer described the situation in one of them:

In places, from time to time, a few landing craft beached. Some broke their backs, crushed as a dog crushes a bone. On Tuesday (the 20th) it blew as hard as ever. Someone said "I reckon this will be the most famous gale since the Armada"... Ships were now dragging their anchors and parting their cables. Any engine failure meant certain disaster. A destroyer struck a mine and drove on shore, and as night fell a big coaster grappled by two tugs bore down on us. Next came a signal "If the ship on your port bow is No. 269, she contains 3,000 tons of ammunition"; but the tugs held her like terriers all night and she was saved.

Many ships and craft spent fearful days and nights in the Gooseberries, fighting hard to prevent themselves being swept onto the shore. Of twelve LCTs (Landing Craft Tank) that had been dispatched to land supplies on Juno Beach but were diverted to the Gooseberry at Courselles, a total of seven would be forced ashore by the wind. Six had their backs broken. It was difficult, exhausting work, and crews greeted the blue skies and low winds that the evening of the 22nd brought with elation.

The storm had a considerable effect on Allied logistics, both directly, during the days it blew, and indirectly, through the damage it did to the Mulberries and the ships it sank. In the days before the gale, an average of 22,570 tons of stores had been unloaded per day. While the storm was blowing, the daily total was 1,800 tons in the British Mulberry. Over the course of the storm, 1,600 tons were landed over the beaches. As a result, between 105-140,000 tons of supplies, and 20,000 vehicles arrived behind schedule. This deficit would not be made up until the 26th July. The pause in offensive operations that the supply deficit necessitated gave German forces in Normandy a chance to consolidate and bring up reinforcements. Over the course of the storm, some 800 vessels had been driven ashore. The destroyer Fury was disabled by a mine, and then thrown on shore, rendering her a total loss. Many more ships had been damaged, including the cruiser Diadem, damaged by a collision with a Rhino ferry. Repair work on the beached ships began swiftly with the deployment of repair parties. In the British beaches, this included the repair ships Adventure and Albatross, which proved invaluable. Of the 800 beached vessels, 600 were refloated on the 8th July (the next spring tide), while 100 more were refloated a fortnight later. Following temporary repairs, many of these would return to the UK for more permanent repairs. This sudden influx threatened to overwhelm British port facilities, but excellent staff work by the Combined Operations Repair Organisation meant that the repair work was carried out efficiently and effectively. The Saint-Laurent-sur-Mer Mulberry had been rendered useless as a harbour; the Arromanches Mulberry survived in better shape, but two and a half miles of floating roadway (intended to serve as piers for the harbour) had been sunk in the storm, delaying its full entry into service. It entered full service on the 19th July, but this was over two weeks behind schedule. However, it is not clear how much this mattered, as the US managed to land more supplies per day across Omaha and Utah beaches after the Mulberry at Saint-Laurent-sur-Mer had been destroyed than they had while it was in operation. The storm did more damage to Allied shipping and the Mulberry Harbours than the Germans managed in the two weeks leading up to it. Between D-day plus 7 and D plus 18 (the storm began on D plus 12, and ended on D plus 16) 118 craft were lost to the weather, and 297 damaged. In the same period, the Germans sank just 27, and damaged 29.