The swimmer was pulled from the water at 12:55 a.m., her crew reported, as a thunderstorm raged and winds and waves tossed her support boats around.
It was the third time in a year that Nyad tried to swim the 103 miles to the Florida Keys, and for a third time she came up short.
Jellyfish stings became too much for Nyad on her 100-mile swim. She was put on a support boat that was heading for Key West. In a blog posting, crew member Candace Hogan wrote that Nyad angrily shook her head after being pulled from the water and planned to return to finish the swim after the storms subsided.
"When can I get back in?" Hogan quoted the swimmer as saying. "I want full transparency that I was out. But I have plenty left in me and I want to go on."
On Tuesday afternoon, Nyad swam ashore from Key West's White Street Pier. She emerged out of the water wobbly after the symbolic swim, saying she was disappointed but didn't feel there was anything she could have done better.
"I'm not going to get that moment I dreamed of for so long," she said.
As she walked on the beach, the crowd sang happy birthday. She turns 63 on Wednesday. After addressing the crowd, she lay on the sand and was given oxygen and intravenous fluids.
Support crews said Nyad was severely sunburned and could barely walk when she was first taken out of the water. She had a special suit to keep the jellyfish from getting to her, but her tongue and mouth became too swollen.
An asthma attack and painful jellyfish stings forced Nyad to quit earlier attempts.
The Associated Press contributed to this story.