Recovery crews used sonar to locate the 34-foot vessel. San Francisco police boats spent much of the day searching near Pier 45.
PHOTOS: Dozens rescued after boat capsizes off San Francisco
By midday, officers dropped an orange buoy marking where they believe the 34-foot Khaleesi is resting.
The coast guard says the owner of the boat has agreed to pay a salvage company to retrieve it.
The most immediate concern for the police and the U.S. Coast Guard is the gallons of fuel that were aboard the power boat.
Once it's recovered, then police will continue their investigation to see if the boat was overloaded and to see if the Khaleesi had enough life jackets for everyone aboard.
One boat captain who responded to the emergency raised immediate concerns. "Honestly, I thought it was overloaded, it was top heavy and had a lot of people on a small boat," said David Griffith.
The Khaleesi went down just after the Blue Angels finished their air show on Saturday.
Mitch Gronner was hosting a party near Pier 45. He says there was a bit of a traffic jam in the water.
"They travel right along the jeddy there, that's their lane, that's their highway. And there's dozens and dozens that go by at a quick clip, and one of the disappeared," said Gronner, with the Aloha Fish Company.
The coast guard tells says the Khaleesi was not a commercial vessel, so they have no passenger safety inspection information.
A total of 30 people were aboard. A 4-year-old, who was pulled from inside the overturned boat, was discharged from General Hospital on Monday.