McCardel, 28, gave up the attempt after 11 hours in the water due to a "severe debilitating jelly fish sting," her support team said in a statement.
"Chloe is now on one of the support vessels heading to Key West. She will spend the next 24 hours recuperating before deciding on her plans going forward," the statement said.
McCardel, who plunged into a calm, crystal-clear sea early on Wednesday, had hoped to swim through the Straits of Florida in about 60 hours and reach Key West on Friday night.
She had a team of scientists in the United States to help guide her through the powerful and unpredictable current that has stymied many previous attempts, and was aware of the hazards posed by jellyfish.
Her swim was timed with the season and moon phase to minimize the presence of the venomous box jellyfish, which had plagued previous swimmers, including American Diana Nyad who was stung repeatedly in August on her fourth failed attempt at the crossing. It was not immediately clear what species of jelly fish ended McCardel's bid.
Only one person, Australian Susie Maroney in 1997, has completed the Cuba-U.S. swim, but she used a shark cage, which helps cut through the water.
Last summer, British-born Australian Penny Palfrey got tantalizingly close to the Florida Keys but could not finish when she swam into a Gulf Stream eddy that pushed her in the wrong direction.
Just before jumping into the sea from a promontory at Havana's Hemingway Marina, McCardel had been sure enough of her success to invite the commodore of the marina to a party in Key West on Friday night.
"(I'm) as confident as I can be ... I think it's all going to work out well," she said.