Officials said the two were walking near the rocks at about 3:15 p.m. this afternoon when they were pulled into the surf.
The mother and child were rescued from the water before firefighters arrived and were taken by paramedics to the hospital in serious condition.
MORE: Man in critical condition after being swept offshore by sneaker waves at Baker Beach, SFFD says
The incident happened hours after the National Weather Service issued a beach hazards statement warning beachgoers of increased risks of sneaker waves and strong rip currents. The advisory remains in effect through early Sunday morning.
Fire officials and witnesses said conditions at Baker Beach can be deceptive, especially near the rocky northeastern end of the shoreline.
"There were a lot of people surrounding her and they got her on a stretcher and had a CPR thing on her face, and I heard them say she caught her breath," said witness Maria Flores.
MORE: Surfer dies at San Francisco's Ocean Beach despite numerous lifesaving efforts
"Baker Beach is deceptive as it is usually not as aggressive as Ocean Beach. But, it does have its inherent hazards," said Capt. Jonathan Baxter. "This occurred near the northeastern portion of Baker Beach, towards the rocky area. Again, part of our safety message is never go on rocks whether there's a beach hazard statement or not."
Firefighters are reminding beachgoers that sneaker waves can strike without warning and can surge much farther up the beach than expected. They urge people to never turn their back to the ocean and to follow warnings from weather officials and first responders.