At the start of World War II, Swordfish was missed with three torpedoes by her sister ship HMS Sturgeon after being mistaken for a German U-boat.

During her sixth war patrol, Swordfish was mistakenly bombed by a British aircraft, but sustained no damage.

She had left Portsmouth Harbour only hours before, and it is assumed that she was carrying out a trim dive when she struck the German mine.

The S-class submarines were designed as successors to the L class and were intended to operate in the North and Baltic Seas.

[3] For surface running, the boats were powered by two 775-brake-horsepower (578 kW) diesel engines, each driving one propeller shaft.

On 14 September, southeast of Aberdeen, Scotland in position 56°22'N, 01°28'W, she was mistaken for a U-boat by her sister ship HMS Sturgeon, which fired three torpedoes.

Informed the next day of the attack of HMS Spearfish, she was ordered to stay away from the area and returned to Dundee on 3 October.

On 20 April, she sighted and attacked a German convoy, made up of Three heavy transports and four escorts in position 58°48′N 10°19′E / 58.800°N 10.317°E / 58.800; 10.317.

Two days later, she sighted another convoy of trawlers and escorts but did not attack them due to their shallow draught, which would have caused the torpedoes to run under the ships.

[5] Nothing was heard from her following her departure from Portsmouth on 7 November 1940 with 40 crew on board to relieve HMS Usk which was on patrol off the Western Approaches near Brest, France.

[8][9] The wreck lies in about 46 metres of water roughly 12 miles south of St. Catherine's Point, Isle of Wight in position 50°24′30″N 01°21′00″W / 50.40833°N 1.35000°W / 50.40833; -1.35000.