The 14-pound pup was caught up against the Mayfield Slough flood gate at high tide, Animal Services Officer William Warrior said.
A passerby heard the pup's cries as the seal bobbed up and down near the concrete wall, its head periodically disappearing under the water.
"We had a concern about the way the baby was struggling," Warrior said. "We were worried about him possibly drowning."
Climbing down the flood gate, Warrior and another officer lifted the black-and-silver pup out of the bay water using a net and brought the seal to the Palo Alto office of Peninsula Humane Society's Wildlife Rescue Center.
From there, the seal was transported to the Marine Mammal Center in Sausalito at about 5:30 p.m. for further care.
Jim Oswald, a spokesman for the Marine Mammal Center, said the female pup, which they've named Floodgate Dolly, is about 5 weeks old. Harbor seal pups are weaned from their mothers when they're between 4 and 6 weeks. The pup probably came from Mowry Slough in Newark, one of the sites nearby where harbor seals gather in groups, he said.
The pup is the first harbor seal from Palo Alto that the center has received since 1991, he said.
Floodgate Dolly appears uninjured. She is resting in the intensive-care unit and has a roommate to help bring her stress level down, Oswald said.
"She's alert but a little emaciated, and she's vocal," he said.
On Thursday Dolly was holding her own and was being tube fed until she can eat fish on her own. She currently weighs about half the normal weight for a pup her age, but she is doing OK, he said.
"She has a way to go to gain weight and strength. She has another harbor seal roommate named Bogey to keep her company. For now, she'll remain in ICU until her health improves enough so that she can go into one of our rehabilitation pools. She's mostly on electrolytes as well as harbor seal formula made of a milk-matrix and salmon oil mixture — a fish smoothie," he said.
Harbor seal pups can become stranded when they are spooked while foraging for food or when they have an underlying problem or illness, Oswald said.
"Nine out of 10 times it's because they were spooked by humans or dogs," he said.
It is pupping season, and the center advises that people don't pick up stranded seals if they are found.
"We remind people that if they come across a sick or injured seal or sea lion, they should give the Marine Mammal Center a call at 415-289-7325 and not pick up or approach the animal. They might still be weaning, and you don't want to separate the pup from mom," he said.
The center, which covers marine-mammal rescue over a 600-mile area from Mendocino to San Luis Obispo counties, is currently inundated with marine wildlife. Food shortages around the Channel Islands in southern California have overloaded rescue centers there.
The National Marine Fisheries Service estimated 1,000 young California sea lions have become stranded. California sea lions wean at 6 to 9 months of age, Oswald said.
The Marine Mammal Center is helping them out and has double the normal number it takes in this year, he said.
"The fish are not there for whatever reason. There have been a lot of mass strandings," he said.
The problem could shift to the Bay Area as the sea lions naturally progress north.
"We're not out of the woods yet. We may see more of these strandings here," he said.
Oswald said people can help the center purchase fish for Floodgate Dolly and other patients.
"This spring we're estimating that we'll go through 80,000 pounds of herring, given the 165 patients we're caring for right now and with more on the way. They can learn how to donate at: www.marinemammalcenter.org/Get-Involved/awareness-campaigns/dollar-a-pound.html."
A video of William Warrior explaining the seal-pup rescue has been posted at http://vimeo.com/63713223