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Both the Royal Navy and the German Navy were unprepared for war. At the outset, Britain re-introduced the convoy system for merchant ships evolved during the First World War, but it did not have enough escort ships and aircraft. Germany had few modern battleships and cruisers. Of the 57 U-boats available, only 39 were immediately operational and only 26 suitable for the Atlantic. Before the war it had been estimated that 300 would be needed to defeat Britain.

In this period, the only threat to shipping on the open seas came from surface raiders. The pocket battleships Deutschland and Admiral Graf Spee were on station in the Atlantic before the outbreak of war ready to harass shipping routes and tie down British forces in their defence. Deutschland accounted for only two ships before being recalled in November 1939. Admiral Graf Spee sank nine ships in the Indian Ocean and South Atlantic before being trapped by three British cruisers off the River Plate, Uruguay on 13 December 1939 and scuttled by her captain four days later. On 23 November, Scharnhorst, on her first joint operation of the war with fellow battle cruiser Gneisenau, had despatched the armed merchant cruiser Rawalpindi in the north Atlantic before slipping back to base at Wilhelmshaven. A small number of disguised merchant raiders, starting with the Atlantis in March 1940, were to range far and wide over the next 3½ years sinking or capturing 133 ships (829,644 tons). Also, from the beginning of the war the Germans launched a campaign of offensive minelaying, by sea and air, which became the third highest cause of Allied shipping losses after submarines and aircraft.

U-boats were deployed in the waters around the British Isles. The small numbers of Commodore (later Rear-Admiral) Karl Dönitz's force which were operational were ready at sea by the end of August. Initially, U-boat commanders were under instructions to adhere to international law when attacking merchant shipping. In practice, however, unrestricted submarine warfare began on the very first day of the war when the passenger liner Athenia was sunk by U-30 on 3 September 1939. Homeward-bound convoys from Canada, West Africa, Norway and Gibraltar, outward convoys from the Thames ports, Liverpool and the Clyde and coastal convoys between the Thames and Firth of Forth were started between September and early November. However, escort ships could only remain with the convoys for the first four hundred miles on either side of the Atlantic. Losses to submarines in the first two months (68 vessels; 288,686 tons) were comparatively heavy as many ships continued to sail independently. But, by the end of 1939, only twelve of the 114 ships lost to U-boats had been sunk in convoy. In October and November, Dönitz had made his first attempts at group attacks. Although these tactics were not successful at this time, they were to become a mainstay of his future strategy.

Other defensive measures, such as minefields in the straits of Dover, Royal Navy patrols in the North Sea and Iceland-Faroe Islands gap and reconnaissance by Coastal Command aircraft all contributed to restricting the German Navy's access to the Atlantic until the middle of 1940. Offensive sweeps against U-boats by aircraft carriers with destroyer escorts, advocated by the First Lord of the Admiralty Winston Churchill, did not prove as successful. The Ark Royal, the Royal Navy's only modern carrier, was nearly lost when attacked by U-39 on 14 September 1939. Three days later, another carrier Courageous was sunk by U-29 in the Bristol Channel at the cost of 518 lives. The submarine threat to capital ships was reinforced on 14 October by Gunther Prien in U-47 when he breached the defences of the fleet base at Scapa Flow in the Orkney Islands and sank the battleship Royal Oak. Escort destroyers hunting for U-boats continued to be a prominent, but misguided, feature of British anti-submarine policy for the first year of the war. The U-boats nearly always proved elusive and the convoys, denuded of cover, were put at even greater risk.

At the beginning of 1940, U-boat successes rose sharply in January and February, though all but a handful of the victims were ships not sailing in convoy. A substantial improvement in the situation from March onwards was due to the withdrawal of most of the U-boats to cover the German invasion of Norway in April. In the first nine months of war, Germany had experienced mixed results in its U-boat campaign. Although his force had sunk nearly 800,000 tons of shipping by the end of April 1940, Dönitz had lost 22 submarines. Overall operational strength had declined and would not increase again for some considerable time.

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