Kingston and a female passenger were injured when the watercraft hit the Palm Island Bridge around 6 p.m. Sunday, Florida Fish and Wildlife Conservation Commission spokesman Jorge Pino said.
The Miami Herald reports that a passing boater saw the accident and took the two on board his vessel.
Both were hospitalized early Monday at Ryder Trauma Center, but Pino said he didn't know their conditions.
Authorities are investigating the crash, and "nothing at this point would indicate that alcohol played a role," Pino said.
Kingston rose to fame with his 2007 hit "Beautiful Girls" and was also featured on songs by artists including Justin Bieber. His self-titled debut album sold over 1 million copies worldwide.
On Twitter, Bieber posted a message of support for Kingston.
"Got my friend Sean Kingston in my prayers tonight," Bieber tweeted early Monday. "A true friend and big bro. Please keep him in your prayers tonight as well."
A number of hip-hop musicians were in Miami Beach over the weekend for Urban Beach Week.
In a 2007 interview with The Associated Press, Kingston described his music as a fusion of reggae, pop, rap and R&B.
"It's Sean Kingston genre. I have my own genre," Kingston told the AP at the time. "No disrespect to no artist or dudes out there. I feel like I am my own person. I am doing my own thing."
His music has been unique among hip-hop offerings, as Kingston refused to use profanity.
"To put it in my music, that's not the message I am trying to send out," he said in the 2007 interview. "That's not the type of artist I am trying to be."