It is believed the 64-year-old was transferring fuel from a jerry can on board an 8m houseboat at the marina's fuel dock area when a pilot light ignited the fuel, about 2.30pm on Monday.
Onlookers watched in horror as the man ran out of the boat covered in flames.
Professional skipper John Nicholson, 54, who works for Coomera Houseboat Holidays, had just moored the vessel he was skippering at an adjacent fuel bowser when he heard a scream.
"I just saw this guy stagger out of his houseboat and he was on fire and the container was on fire," he said.
"His feet, hands, upper body, and head looked like they were on fire.
"I've never seen a person burning before, not in real life."
Mr Nicholson grabbed a fire extinguisher and ran to help.
By that stage, the burning man had leapt into the water to extinguish himself, dropping the flaming container of fuel next to the bowser.
Mr Nicholson managed to put out the fire, while two women who were also onboard made their way off the vessel safely.
""He was trembling and he wanted to go back and tidy up his boat, but obviously shock was starting to set in.
"He probably had burns of about five to six inches long and three inches wide and on one foot the skin had burnt off a couple of layers.
"He had patches on his arm, and it looked like his upper body had been burnt -- some of the skin had started to burn away."
He was taken by ambulance to Gold Coast Hospital in a stable condition.
An ambulance spokeswoman said he had burns to his feet, shoulders and arms.
Marina general manager Steve Sammes said the fire was an accident.
"He started to decant fuel from a jerry can into the outboard petrol tank inside the boat and he spilt some of the fuel whilst decanting it," he said.
"Inside the boat there is a gas fridge with a pilot light so the vapour from the spill was ignited by the pilot light of the fridge.
"He had third-degree burns to his left lower leg, his left hand also had third-degree burns and there was scorching to his right and left arm."
Mr Sammes said the man had been holidaying with family from Casino, NSW.
"He was a colleague of the boat owner and was staying on board with relatives for Christmas," he said.
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