The French Navy had a relatively limited role in the Battle of the Atlantic. The German U-boat offensive was, until the fall of France in 1940, confined to the waters around the United Kingdom, while the French Navy had few anti-submarine capabilities. Between the start of the war and the French surrender, none of the 24 U-boats sunk would be sunk by French forces. Similarly, the Kriegsmarine made few attempts at surface raiding before the French surrender. Following this, Free French forces did join the British in escorting convoys, but they were greatly outnumbered by the British, Canadian and, later, American fleets.

In the run-up to war, the British and French Admiralties began to hash out a cohesive strategy. Joint staff talks were held during the 1935 Abyssinian Crisis, and on regular intervals during the Spanish Civil War. In 1938, provisions were put in place for the exchange of liaison officers in the event of war or serious crisis. From the 30th March 1939, as war with Germany began to loom large in the minds of British and French leaders, a series of meetings were held at high levels between the two admiralties. Over the course of seven meetings, the RN and French Navies produced a strategy for fighting the war at sea.

The RN was highly focused on trade protection. The French Navy, protecting a country that relied less on imports (and relied highly on neutral ships to carry imported cargoes), was less so. It had considerably fewer ships suitable for anti-submarine warfare (ASW) and escorting convoys, as well as less experience and training in ASW operations. The French had been planning to rely on independent sailings, which the experiences of WWI had shown to be highly vulnerable to unrestricted submarine warfare, while the British were planning to introduce the safer convoy system as soon as possible. To bridge this gap, the two forces agreed that the British would provide escorts for all oceanic convoys. The French would escort one in every four coastal convoys running from the arrival points in the South-West Approaches through the English Channel. The British would provide sonar equipment and ASW training to the French, as well as licensing the design for the 'Flower' class corvettes to French shipyards. The French Navy also agreed to assist the British in re-establishing the Dover Barrage, a barrier of nets and minefields which had proven an effective anti-submarine block in WWI.

Responsibility for other surface forces was more mixed. The majority of the French forces were to be held in the Mediterranean in the event of war with Italy. There was to be little collaboration with Britain's Mediterranean Fleet. The Force de Raid, built around the large cruisers/light battlecruisers Dunkerque and Strasbourg, was formed at Brest to hunt German surface raiders. Again, this was held mainly under French, rather than joint command. There were just two areas where joint forces were to be formed. In the Indian Ocean, two French sloops would join Eastern Fleet, while an anti-raider group was to be formed at Dakar using French cruisers and a British carrier.

At the start of the war, two German surface raiders were at sea, both 'pocket battleships'. In the North Atlantic was the Deutschland, while her sister ship, the Graf Spee was further south. The Force de Raid made a sortie to cover the minelaying cruiser Pluton, which was to lay a field off Casablanca to dissuade German raiders. However, the operation would be cancelled.

On the 30th September, the Graf Spee sank the British merchant Clement, announcing her presence at sea to the Allies. The Strasbourg was dispatched to meet the British carrier Hermes and a few French cruisers at Dakar, forming Force X. Force X made several futile sorties into the Atlantic during October-November 1939. On the 21st November, Strasbourg was withdrawn back to France along with the heavy cruiser Algerie. Force X, reinforced by the British light cruiser Neptune, would sortie again on the 7th December, putting them at sea on the 13th, when three British cruisers engaged Graf Spee at the Battle of the River Plate. Following this, she was forced to seek shelter in Montevideo Harbour. The short-ranged French ships returned to Dakar to refuel, so they could give chase in the event Graf Spee broke out and headed north. This proved to be unnecessary, as she would be scuttled on the 17th. Force X made a final sortie on the 30th January, following which the French cruisers Dupleix and Foch escorted a convoy northwards and returned to France. Force X was replaced by Force Y, built around the old battleship Provence. This made a few brief sorties in the spring of 1940. These convoys were also escorted by the battleship Bretagne and the Algerie. Force Y would leave Dakar on the 11th April.

In the North Atlantic, things were similarly quiet for the rest of the Force de Raid. The presence of the Deutschland was discovered on the 21st October. This led to suspicions that she might attack convoy KJ3, running from Kingston to the UK, which was in the right area at the time. Dunkerque, two cruisers and three destroyers sortied on the 22nd to protect the convoy. No attack was forthcoming. On the 23rd November, the German large cruisers/light battlecruisers Scharnhorst and Gneisenau sank the British armed merchant cruiser Rawalpindi north of the Faroe Islands. Two days later, the Force de Raid would join up with HMS Hood to patrol the Denmark Strait, returning on the 3rd December. After this, they would make few sorties. Following the German invasion of Norway, the cruiser Emile Bertin would be sent north to join the RN, along with a few destroyers. She would take minor bomb damage on the 19th April, and was replaced by the Montcalm. On the 3rd May, while the Allies were evacuating Namsos, the destroyer Bison was sunk by a German bomber. Several French destroyers would participate in the Dunkirk evacuation, with the Foudroyant and L'Adroit being sunk by aircraft, the Bourrasque being sunk by a mine and the Scirocco and Jaguar being sunk by torpedo boats. Two more destroyers, the Orage and Chacal, would be sunk off Boulogne by aircraft at a similar time.

One of the more active roles taken by the French Navy during this period was the shipping of gold to Canada. This was done to purchase war materiel, especially aircraft, from the USA. The first such shipment was carried out by the cruisers Marseillaise and Jean de Vienne in November 1939. On the 11th December, the Dunkerque and cruiser Gloire provided an escort for a convoy carrying gold to Canada. On their return, they covered seven liners full of Canadian troops of the 1st Canadian Division. In March-April 1940, a cruiser from Force Y, the Colbert, would be detached to join the escort of another convoy to Canada, and a return convoy carrying American planes. As German troops began to storm across France, the French Navy hurriedly evacuated the remaining gold reserves. On 21st May, the Jean d'Arc and Emile Bertin left France with 212 tonnes of gold, along with the carrier Bearn with 194 tonnes aboard. The Emile Bertin would bring across another 290 tonnes of gold on the 12th-18th June, though this would not be unloaded, and the ship sailed for Martinique on the 21st.

The French surrender on the 22nd June 1940 brought an end to the participation of much of the French fleet in the war. This was confirmed by the British Operation Catapult; this aimed to seize French ships in British ports, and prevent the Axis getting their hands on any French ship outside them. You can read more about these operations, including the British bombardment of French ships at Mers-el-Kebir and Hermes' attack on Richelieu at Dakar here and here. The Free French would operate a number of the ships seized in British ports, as well as British ships transferred to the Free French Navy. These ships operated alongside the RN, RCN and other Free navies in protecting convoys across the Atlantic. Two Free French corvettes would be sunk by U-boats; the Alysse on the 9th February 1942, and the Mimosa on the 9th June 1942.The British-built destroyer La Combattante would be sunk by a mine off the British coast in February 1945. In return, the Free French would sink five U-boats (one of which was in the Mediterranean). The Aconit was the most successful. This corvette would claim two U-boats (U-444 and U-432) on the 11th March 1943. The destroyer Leopard sank U-136 on the 11th July 1942, while the corvette Lobelia sank U-609 on the 7 February 1943. The Vichy French fleet would remain in port, mainly in Toulon (though some forces in Algeria would engage Allied ships during the Torch landings), until the German invasion in November 1942. As German forces moved in to capture the fleet, the French sailors scuttled their ships.