During the Second World War, although British anti-submarine efforts were disorganized and ineffectual at first, Sunderlands quickly proved useful in the rescue of the crews from torpedoed ships. On 21 September 1939, two Sunderlands rescued the entire 34-man crew of the torpedoed merchantman Kensington Court from the North Sea. As British anti-submarine measures improved, the Sunderland began to inflict losses as well. A Royal Australian Air Force (RAAF) Sunderland (of No. 10 Squadron) made the type's first unassisted kill of a U-boat on 17 July 1940.
During its service the Sunderland Mark I received various improvements. The nose turret was upgraded with a second .303 (7.7 mm) gun. New propellers together with pneumatic rubber wing de-icing boots were also fitted.
Although the .303 guns lacked range and hitting power, the Sunderland had a considerable number of them and it was a well-built machine that was hard to destroy. On 3 April 1940, a Sunderland operating off Norway was attacked by six German Junkers Ju 88 fighters. It shot one down, damaged another enough to send it off to a forced landing and drove off the rest. The Germans are reputed to have nicknamed the Sunderland the Fliegendes Stachelschwein ("Flying Porcupine") due to its defensive firepower.
Sunderlands also proved themselves in the Mediterranean theatre. They flew many evacuation missions during the German seizure of Crete, carrying a surprising number of passengers. One flew the reconnaissance mission to observe the Italian fleet at anchor in Taranto before the famous Royal Navy Fleet Air Arm's torpedo attack on 11 November 1940.
New weapons made the flying boats more deadly in combat. In 1939 during an accidental fratricidal attack, one 100 lb anti-submarine bomb hit the British submarine Snapper doing no more damage than breaking its light bulbs; other bombs had reportedly bounced up and hit their launch aircraft. In early 1943, these ineffective weapons were replaced by Torpex-filled depth charges that would sink to a determined depth and then explode. This eliminated the problem of bounce-back, and the shock wave propagating through the water augmented the explosive effect.
While the bright Leigh searchlight was rarely fitted to Sunderlands, ASV Mark II radar enabled the flying boats to attack U-boats on the surface. In response, the German submarines began to carry a radar warning system known as "Metox", also known informally as the "Cross of Biscay" due to the appearance of its receiving antenna, that was tuned to the ASV frequency and gave the submarines early warning that an aircraft was in the area. Kills fell off drastically until ASV Mark III radar was introduced in early 1943, which operated in the centimetric band and used antennas mounted in blisters under the wings outboard of the floats, instead of the cluttered stickleback aerials. Sunderland Mark IIIs fitted with ASV Mark III were called Sunderland Mark IIIAs. Centimetric radar was invisible to Metox and baffled the Germans at first. Admiral Karl Dönitz, commander of the German U-boat force, suspected that the British were being informed of submarine movements by spies. In August 1943, a captured RAF airman misled the Germans by telling them that the aircraft were homing in on the signals radiated by the Metox, and consequently U-boat commanders were instructed to turn them off.
The Germans responded to Sunderland attacks by fitting U-boats with one or two 37 mm and twin quad 20 mm flak guns to fire back at their attackers. While Sunderlands could suppress flak to an extent by hosing the U-boat with their nose turret guns, the U-boats had the edge by far in range and hitting power, and firing accuracy. Attempting to shoot down Allied aircraft did, however, prolong the U-boat's presence on the surface, which made the sinking the vessel easier. Nonetheless, fitting of substantial arrays of anti-aircraft guns temporarily decreased U-boat losses while both Allied aircraft and shipping losses rose. As a countermeasure to the increased defensive armament of the U-boats, the Australians fitted their aircraft in the field with an additional four .303s in fixed mounts in the nose, allowing the pilot to add fire while diving on the submarine before bomb release. Most aircraft were similarly modified. The addition of single .50 inch (12.7 mm) flexibly mounted M2 Browning machine guns in the beam hatches behind and above the wing trailing edge also became common.
The rifle calibre .303 guns lacked hitting power but the Sunderland's defensive armament was nonetheless formidable. The aircraft's capacity to defend itself was demonstrated in an air battle between eight Junkers Ju 88C long range heavy fighters and a single Sunderland Mark III of No. 461 Squadron RAAF on 2 June 1943. This was one of several stories of the type's operations related by author Ivan Southall, who flew in Sunderlands during the war. There were 11 crewmen on board the Sunderland: nine Australians and two British. The aircraft was on an anti-submarine patrol and also searching for remains of BOAC Flight 777, an airliner that had left Lisbon the day before and had subsequently been shot down over the Bay of Biscay, killing 17, among them, the actor Leslie Howard. In the late afternoon, one of the crew spotted the eight Ju 88s. Bombs and depth charges were dumped and the engines brought to maximum power. Two Ju 88s made passes at the flying boat, one from each side, scoring hits and disabling one engine while the Sunderland went through wild "corkscrew" evasive manoeuvres. On the third pass, the dorsal turret gunner shot down a Ju 88. Another Ju 88 disabled the tail turret, but the next one that made a pass was hit by both the dorsal and nose turrets and shot down. Another destroyed the Sunderland's radio gear, wounding most of the crew to varying degrees and mortally wounding one of the side gunners. A Ju 88 tried to attack from the rear, but the tail turret gunner had regained some control over the turret and shot it down. The surviving Ju 88s continued to attack, but the nose gunner damaged one of these, setting its engines on fire. Two more of the attackers were also hit and the final pair disengaged and departed, the only two to make it back to base. The Sunderland had been heavily damaged. The crew threw everything they could overboard and nursed the aircraft back to the Cornish coast, where pilot Colin Walker managed to land and beach the aircraft at Praa Sands. The crew waded ashore, carrying their dead comrade, while the surf broke the Sunderland up. Walker received the Distinguished Service Order and several of the other crew members also received medals. With the exception of Walker, the crew returned to Sunderlands - they disappeared without trace over the Bay of Biscay two months later after reporting that they were under attack by six Ju 88s.
On 2 June 2013, a memorial was opened on the green at Praa Sands.