Tourists spotted the injured animal on Friday.
Wire or netting was wrapped around his snout and what looks like a rope wrapped around his neck.
Some tourists say they were there for hours calling for help, but no one came.
Finally, around midnight Erin Brodie, a coordinator from the Marine Mammal Center, showed up to take a look and to get an earful from onlookers waiting for a rescue.
"Those docks are extremely slippery," said Brodie. "Human safety would be at risk and also the animals safety because we can't see what's around there. We can see if there's hooks or lines. If we netted that animal and a hook got around one of those lines and we caused further damage to it because we couldn't see what was going on, that would make us feel terrible. We want to do what's best for this animal."
The injured sea lion was spotted early Saturday morning but slipped back into the water and has not been seen since. On Saturday, Marine Mammal Center rescuers set out in a boat searching for the sea lion, hoping to rescue it.
Pier 39 sea lions have been in the news lately because they seem to be abandoning their perch at the tourist pier. It was unusual to see any sea lion on tha docks on Friday.