There is no body of water "under" the Golden Gate Bridge in the sense of a lake or river beneath a span. The bridge crosses the Golden Gate Strait—the entrance to San Francisco Bay from the Pacific Ocean.
The bridge's towers stand on the shorelines (south pier on rock, north pier on serpentine bluff). The central span (1,280 m / 4,200 ft) clears the navigation channel. Water flows past the towers, not "under" them in a confined sense.