I do not read anywhere in the laws that specifically says drones cannot fly over marine life, as you are stating. If you're saying drones can't fly over protected areas in San Francisco, that's an entirely different conversation. There are many areas around the country and world that are protected or restricted, for many various reasons.

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Otherwise, it clearly states manned aircraft must maintain 1000ft. Unmanned aircraft are permitted to fly anywhere that isn't protected (such as the area of Hawaii with the Humpback whales, or this county coastline you are talking about) as to not disturb the wildlife. Otherwise, there's no specific law that restricts what we're seeing in OP's photo.