The 21-year-old is believed to be in a critical condition after being rushed for assistance with a female passenger.
Kingston collided with a bridge at 6pm local Florida time.
Some 18 hours before he took to the water, he tweeted to his 1.6 million followers: "South beach... #nicee... bout to get fresh and cause that movie!!..."
Kingston's representative confirmed: "Sean Kingston was in an accident today. No further details are available at the moment. He and his family thank everyone for the well-wishes."
Justin Bieber, a close friend who collaborated with the star for 'Eenie Meenie', wrote on Twitter: "Got my friend @seankingston in my prayers tonight. a true friend and big bro. please keep him in your prayers tonight as well."