According San Francisco Fire Department, the body was discovered west of Treasure Island at 1:02 p.m. Officers recovered the body from the water and later declared the individual deceased on scene.
The body has not been identified and police have not disclosed sex or any other identifying features.
Any connection to Tuesday's boat disaster in the same area, where one person died and three remain missing, has not been established at this time.
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"At this point, we cannot confirm that that particular person is in any way, shape or form related to the boat accident that happened... medical examiners are working to identify the identification of this person, and they will determine the identity after they talk to the next of kin," said Lt. Mariano Elias with the San Francisco Fire Department.
Elias said, while it is possible this can be one of the three missing from the boat disaster earlier this week, it is too early to tell.
"Unfortunately, we do have several jumpers from the Golden Gate Bridge often, and we don't want to confuse one with the other until we get full clarification," he said.
He said the fire department is very busy with all types of water rescues, "including swimmers, jumpers, people who are under some kind of influence of something and kite surfers."
According to SFFD, it will take one to two days before the Medical Examiner determines an ID or any connection to Tuesday's events are made.
Stay with ABC7 Eyewitness News for the latest details on this developing story.