The advisory was issued after "confirmed aggressive shark behavior in the vicinity of T-Street Beach," according to a statement.
"The beaches will remain open, but water access will remain closed until 8:00 p.m.," the statement said, "pending no additional shark sightings."
Just before 8 p.m. Sunday, a couple of surfers near T-Street beach reported seeing a dark shadow lurking around them.
Leo Pinto said he spotted a shark from the shore.
"It was a shark about 6-7 feet roaming around, going back and forth," he said.
"Moments later the one surfer was knocked off his board by what appeared to be a shark," San Clemente Marine Safety Lt. Sean Staudenbaur said.
"There's no injuries to the surfer," Staudenbaur said. "But with that aggressive behavior we follow the Orange County shark protocol that lifeguard agencies have adopted, and we are doing a 24-hour closure one mile north and south of the location."
The bumping incident left a surfboard dented.
San Clemente Councilmember Chris Duncan said keeping people out of the water is necessary.
"We want to make sure it's completely safe for our residents. We don't want there to be any incidents out there," he said.
There were no immediate reports of injuries.
Video from AIR7 HD showed a lifeguard boat patrolling the water off San Clemente, where the sand was crowded with beachgoers on Memorial Day.