Lorenzo Veloz, a spokesman with the Florida Fish and Wildlife Conservation Commission, said Fernandez was one of three men who died in the boating accident.
Fernandez, 24, was finishing his best major league season, going 16-8 with a 2.86 ERA. He was an all-star for the second time.
He was set to start at Monday's Marlins game against the Atlanta Braves.
The Marlins released the following statement Sunday:
The Miami Marlins organization is devastated by the tragic loss of Jose Fernandez. Our thoughts and prayers are with his family at this very difficult time.
Today's game against the Atlanta Braves has been cancelled.
Marlins officials learned of the death just before 7 a.m. The team met at 10:30 a.m.
"Sadly the brightest lights are often the ones that extinguish fastest," Marlins President David Samson said. "His personality transcended culture and religion and race. His story will be told forever."
General Manager Michael Hill was in tears at the news conference held by the Marlins in response to Fernandez's death. Manager Don Mattingly and third baseman Martin Prado sat at the microphone with Samson and Hill.
Mattingly struggled to speak at the news conference: "I see such a little boy in the way he played. Just joy in him when he played," he said.
"They way Jose played and the way he was on the field that how these guys can honor Jose," Samson said.
The team will play its regularly scheduled game Monday night against the New York Mets at Marlins Park.
"We are devastated by the news that José Fernández has tragically passed. José was a remarkable young man and a tremendously gifted athlete, who, at just 24, established himself as one of the game’s biggest and brightest stars," Major League Baseball Players Association Executive Director Tony Clark said in a statement. "Our thoughts and prayers go out to José’s family, friends, teammates, Miami Marlins organization and legions of fans in the United States and Latin America."
Numerous photos on Fernandez's Instagram page show a love for boating and fishing. According to one of the last photos he posted, on Sept. 19, he was expecting a child with his partner.
The Cox Media Group National Content Desk contributed to this report.
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