The animals come and go regularly, leaving in the fall to breed and birth their young in the Channel Islands.
Last fall, however, something unusual happened. After ballooning to a population of 1,700 animals layered two and three deep on the docks, the sea lions departed as if following orders, leaving behind only a few stragglers.
Marine experts believe the animals might have traveled 500 miles north, looking for fish and colder waters along the Oregon coast.
Now they are coming back to San Francisco for equally mysterious reasons -- but not in their usual numbers. An estimated 80 or so animals were in the area last week -- a drop from the typical 200 to 400 sea lions this time of year.
Only a couple dozen animals lounged Tuesday on the floating docks, barking and diving as if aware of their role as local celebrities.
Ryan and Wylie Geldert of Bunbury, Australia, stopped by the pier three times in a week looking for sea lions and were glad to finally catch a glimpse of the San Francisco icons.
"The sea lions are pretty famous," said Ryan Geldert. "We would have been disappointed not to see them."
Visitors have been wondering what happened to the animals.
"That's the million-dollar question," said Jim Oswald of the Marine Mammal Center, which has an information kiosk staffed by volunteers at Pier 39.
"Our guess is, there was no food. I have to emphasize it's a guess," he said.
Biologists at Sea Lion Caves, a private preserve near Florence, Ore., said big groups of sea lions started to show up in October, about the same time they started leaving Pier 39.