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The closure comes after two people were bitten by a sea lion in the area within 24 hours.
The latest attacked happened at 8 a.m. Friday.
"I hear these screams from right at the head of the entrance to the harbor," described Rainier Billingsley. He was onboard a friend's sailboat when he heard the man's distress call.
VIDEO: Second sea lion attack at San Francisco's Aquatic Park
That's when nearby swimmers with the Southend and Dolphin clubs went to the man's aid.
Officials say he was taken to the hospital with a bite wound near the groin but is expected to be okay.
Given that this was the second sea lion attack in less than 24 hours, they're not taking any chances. The Golden Gate National Park Service posted signs along the beach of the Aquatic Park, informing the public of the danger. The area will be closed to swimmers until Monday.
"A lot of people may think this is their backyard, you live in the city but really, you're entering into the wilderness," said Lynn Cullivan, public information officer with the National Park Service.
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Park Rangers say incidents like this are extremely unusual. The last time people were bitten by a sea lion near San Francisco was about 11 years ago, also at Aquatic Park.
While the danger signs may not keep everyone out of the water, park rangers caution to enter only at your own risk.