The Coast Guard got a call at about 3:30 p.m. from the crew of the ferry Old Blue, who saw the boaters in the water near Aquatic Park, Coast Guard Lt. J.G. Nicole Emmons said.
A Coast Guard crew responded to help marine police rescue the 16 who were taken to hospitals as a precaution, Emmons said. No significant injuries were reported.
Those on board think the strong wind were to blame.
"We weren't able to get the sails down or an anchor out, which meant it just flipped over again, so at that point, we had everyone go back to the other side of the boat and hold on," explained Greta Hull the Sea Scouts adult lead.
"They looked to be afraid and scared so we quickly moved in, threw in a heavy line, which we hold on to and allow persons in the water to grab on to," said Assistant Fire Chief Lorrie Kalos with the San Francisco Fire Department.
Everyone on board were wearing lifejackets, but the kids were in the 55 degree water for more than 15 minutes. Medics were concerned hypothermia might set in.
"You always worry about the youngest ones, but if you had some non-swimmers out there, the panic alone could throw them into a tizzy," said Kalos.
The boat became grounded at Kirby Cove near the Marin Headlands.
Most had some sailing experience. The sea scouts go out weekly.
This is the first time a sea scout boat has capsized in the Bay in more than two decades. However, on Thursday, the Coast Guard helped rescue 15 people from a 50-foot sport fishing boat that took on water near the Golden Gate Bridge.