The 21-year-old was riding with a female passenger Sunday when he apparently slammed into the Palm Island Bridge near Miami Beach at about 6 p.m. Both were thrown into the water from the Sea-Doo watercraft, which is similar to a Jet Ski.
A passing boater, Jimmy Vega, and friends saw the accident and took the two on board his vessel.
"I jumped in the water and helped him keep his head above water," Vega said. "One of our girlfriends got on the phone and started calling police.
Vega said he had no idea it was the famous singer he was rescuing.
"As we approached, we saw their faces in shock," he said. "You just don't think in a moment like that, you just try to help."
Rescue crews then transported the two to Jackson Memorial Hospital.
The full extent of Kingston's injuries was unknown, but the passenger was alert and talking to investigators.
"I don't know exactly what caused the accident, that's going to be something that we're looking into," said Jorge Pino of Florida Fish and Wildlife. "Our investigators are trying to interview the young lady that was a passenger and we're also trying to get information from witnesses that may have been in the area."
Authorities said there was no indication that alcohol played a role.
Kingston had a big hit with the song "Beautiful Girls" and recently toured with pop star Justin Bieber.
The singer was born in Miami but grew up in Jamaica and has a home in South Florida.
Bieber tweeted, "Got my friend @seankingston in my prayers tonight. A true friend and big bro. Please keep him in your prayers tonight as well."
Kingston's life vest was still floating near the accident scene Monday. According to witnesses, it had fallen off him.
The Associated Press contributed to this report.