San Francisco Bay is a body of water lying adjacent to the city of San Francisco on Earth. It is spanned by 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)