The death was the first in the event's 33-year history.
The race begins with a 1.5 mile swim from the island home of the former federal prison. That's followed by an 18-mile bike ride and an 8-mile run through Golden Gate Park and the San Francisco coast.
Bill Burke, the race's director, said the water's cold temperatures did not contribute to the man's heart attack.
"Was it colder than normal? Yes. But in my opinion, the water temperature was not a factor at all in this tragedy," Burke told the San Francisco Chronicle. "The gentleman obviously had a heart condition he was unaware of."
Officials reportedly pulled the unidentified man from the water and performed CPR to no avail.
The race is typically held in June but was pushed-up to March this year due to conflicting schedules with a yachting event.
The Associated Press contributed to this report.