A marine unit from the Police Department spotted the body in the Bay at 10:37 a.m. off of the pier just south of AT&T Park, police spokesman Officer Albie Esparza said.
No information about the gender or identity of the body was immediately available Thursday morning.
Esparza said, "It appears the body had been in the water for a while."
The case has been handed over to the medical examiner's office, which will determine whether the death was a suicide or suspicious.
City officials announced this week that Pier 48 will soon be the home of a new Anchor Brewing restaurant as part of the Mission Rock development owned by the San Francisco Giants.