Pier 39 sent ABC7 News video of the rescue.
It shows a crew using a net to get the animal out of the water and into their boat.
Rescuers say they likely got her out "just in time."
This was all in response to reports around 10:45 a.m. about a coyote pup in the area.
There was no information given on the animal's condition.
VIDEO: Coyote explores Kirby Cove beach near Golden Gate Bridge