Franky Zapata plunged into the water about half way through his record-breaking bid.
The 40-year-old one-time Jet Ski champion missed a landing platform mounted on a boat as he tried to pause for a planned refuelling.
It came about 10 minutes into what would have been a 20-minute crossing of the 22-mile stretch of water between Calais and St Margaret’s Bay near Dover.
A member of his team told The Guardian the waves, whipped up by an unusually strong wind, had caused the one-metre-square landing platform to shift slightly as Mr Zapata came down for the two-minute pause.
“We’re talking about a few centimetres,” the crew member said. “It’s an enormous disappointment … but he will definitely try again.”
Mr Zapata, who is credited with inventing the flyboard, had been aiming to keep an average speed of 87mph while travelling at just 15 metres above the water.
The challenge was taking place today to mark 110 years since Louis Bleriot made the first plane flight across the Channel in 1909.
Shortly before taking off, the adventurer had told reporters that making the crossing was “a boyhood dream”.
He said: “We created a new way of flying. We don’t use wings. You are like a bird, it is your body that is flying. It is a boyhood dream.”
But he also warned, prophetically as it turned out, that the wind could make completing his journey more perilous and that success was not guaranteed.
Mr Zapata received widespread attention following France’s annual Bastille Day parade in Paris earlier this month, when he took part in a military display on his flyboard.
The device is powered by five jet engines and fuelled by kerosene kept in the rider’s backpack.
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