Rainwater is dripping into the steel structure below the road deck on the suspension stretch of the span. That stretch is supposed to be watertight.
Independent engineers say the water poses a risk of corrosion, which could make the structure thin and weak and significantly shorten its life span.
Caltrans crews were on the bridge Sunday assessing the problem.
"This was completely anticipated," Bridge spokesperson Andrew Gordon said. "And again, this would be an issue if we weren't expecting it, if the inside of that deck was not primed to protect it, if we didn't have weepholes, if that water went undiscovered and just sat there, but none of that has taken place."
Bridge engineers point out that everything needs maintenance, because no bolting system will ever prevent water from coming in.
The bridge cost $6.4 billion and is supposed to last well into the 22nd century.
(The Associated Press contributed to this report)