The 62-year old American author/journalist had been in the water for 60 hours and was about halfway through her swim from Cuba to Florida when she was continuously stung by jellyfish.
In addition a major lightning storm that was taking place in the vicinity of Nyad and her team had put them in extreme danger, Nyad's operations chief Mark Sollinger told reporters.
"With all the threats continuing, Diana decided that it was not a risk that we wanted to take," Sollinger said.
On Tuesday morning Sollinger told CNN's Soledad O'Brien that Nyad's lips and face are swollen, but she is holding up "as well as someone who just spent 63 hours" performing a "monumental and extremely dangerous" feat.
Despite falling short of completing 103 mile swim, Sollinger described Nyad's achievement as "huge," despite having to stop before she reached Florida.
"It's a cross between being down, being so tired because everyone wanted this so much, and a huge sense of accomplishment," he said. "Nobody in the world would even attempt this, but we did."
Nyad, who was making her fourth attempt to swim across the Straits of Florida, was stung by jellyfish on her lips, forehead, hands and neck on Saturday night.
The following evening, a windstorm threw the New York City native off course.
"There is lots of lightning out there and the storm is blowing right on top of Diana," a blog post stated early Monday, adding that the swimmer was safe and "feeling strong."
While Nyad's failed to complete her first attempt at the swim in 1978, she tried again twice in 2011. Her efforts ended after an 11-hour asthma attack and multiple jellyfish stings.
Confident that 2012 would be her year, Nyad insisted Friday she was ready to try it again. "I'm feeling tremendous inner pressure that this has got to be it, this has got to be the last time," she said.
Nyad was reportedly swimming without a shark cage, dependent on on electronic shark repellent and a team of divers to keep the predators away.