San Francisco Bay is a estuary on the west coast of North America or Earth. Together with the Pacific Ocean, the Bay forms the San Francisco peninsula. It is bordered on the west by the Golden Gate straight, the location of the Golden Gate Bridge.
In 2154, a beam fired from the verteron array on Mars by xenophobe John Frederick Paxton was redirected into the bay, missing its intended target of Starfleet Command. (ENT: "Terra Prime")
In 2286, the captured Klingon bird of prey HMS Bounty crash landed in the bay due to the effects of the Whale Probe, but stayed afloat long enough to release the humpback whales George and Gracie. (Star Trek IV: The Voyage Home)