The sightings of whales are becoming more common as they begin migrating south to warmer Mexican waters.
Tourists aboard the Kitty Kat left early Thursday morning for the Farallon Islands, hoping to catch a glimpse of a whale or two.
They got more than they paid for -- a close up look at this humpback whale inside the bay.
"All of a sudden we saw a spout of water and then the tail flipped out of the water and it was just amazing," tourist Gary Turner said.
It even surprised Captain Joe Nazar, who has been piloting tours in these waters for three decades.
"There was a humpback whale performing a fluke and also being able to do its blows directly under the Golden Gate Bridge," Nazar said.
The ocean just outside the bay is a major migration route for whales so sightings are not unusual, but this one was.
"It's extremely unusual for a humpback whale to come in San Francisco Bay," Stan Minasian said. Minasian is a naturalist with the Oceanic Society. He thinks Thursday's humpback may have just been exploring.
"When they get into the bay and find out there's no food, it's very shallow and there's a lot of noise in the bay from the ships, they turn around and go out," Minasian said.
Minasian says he has recently seen large pods of humpback whales around the Farallons. Two weeks ago Minasian counted 64 humpbacks in one day.
"In all the trips we've done in the Farallons, which are hundreds and hundreds of them, this is by far a record for us, the boat was surrounded by humpback whales," he said.
Minasian says the reason for the large number of humpbacks may be this year's abundance of krill -- the small crustaceans which they feed on.