The explosion resounded across the capital, killing 300 and shocking Samuel Pepys and all who heard of it that cold March morning in 1685.

HMS London, a royal warship, had left Chatham Docks and was shouldering her way up the Thames to pick up her captain when, without warning, she exploded.

Naval historians have been mystified about the cause, one theory being that an unstable mix of chemicals ignited the ship’s supply of gunpowder.

Now a 20-year study of another 17th-century warship has blamed instead the personal habits of the men on board: in particular their tendency to relieve themselves into the deepest recesses of the ship.

The theory suggests that rotting faeces in the bilges led to a build-up of methane that could have been ignited by a candle below decks.

Richard Enser, an engineer and naval historian, arrived at this explanation while researching the Lennox, launched a decade after the London exploded. Restoration Warship, to be published in the new year, takes the Lennox as the archetypal ship of the period. Among her records was an account of a curious incident, recorded while she was laid up at Chatham.

The ship’s lieutenant fell down the well, an aperture running from the top deck beside the mast to the bottom of the hold, through which the crew could pump out the bilges. It appears that the skeleton crew had been using the well as a lavatory, rather than relieving themselves over the side as they would have done at sea. When two sailors were sent to find the fallen lieutenant, according to the report, “they were rendered in a manner dead by the stench”.

Mr Enser told The Times: “They were unconscious. Of course, it is not the smell that makes you unconscious, it’s the methane.” This, he thought, could be the cause of many ship explosions reported in the 17th century.

“When you have that concentration of methane, all it would take is someone being sent down there with a lantern to set it off,” he said. “The powder room is in the hold as well.”

Charles Trollope, an authority on naval ordnance from the period, prefers the theory that the explosion occurred as the crew were reloading old cartridge papers with gunpowder in the magazine, a common practice. “When they stopped using secondhand cartridge papers there were no more explosions,” he said. “Then again it could have been the two things together.”

Pepys’s account

“Though a bitter cold day, yet I rose, and though my pain and tenderness in my testicle remains a little, yet I do verily think that my pain yesterday was nothing else, and therefore I hope my disease of the stone may not return to me, but void itself in pissing, which God grant, but I will consult my physitian. This morning is brought me to the office the sad newes of “The London,” in which Sir J. Lawson’s men were all bringing her from Chatham to the Hope, and thence he was to go to sea in her; but a little a’this side the buoy of the Nower, she suddenly blew up. About 24 and a woman that were in the roundhouse and coach saved; the rest, being above 300, drowned: the ship breaking all in pieces, with 80 pieces of brass ordnance. She lies sunk, with her roundhouse above water. Sir J. Lawson hath a great loss in this of so many good chosen men, and many relations among them. I went to the ’Change, where the news taken very much to heart. So home to dinner, and Mr Moore with me. Then I to Gresham College, and there saw several pretty experiments . . . about 11 home to supper and to bed."

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