The highway bridges are heavily used, but the southern shores of San Francisco Bay are mostly either salt ponds or swamps and marshes under protection orders (this is also why there’s no on-campus housing at the Googleplex), with nothing much in walking distance.

There’s a proposal to build a ferry terminal in Redwood City, but that’s still pretty far from the densest part of the south bay.

There are water taxis, but I think they only go along the SF waterline, between say Fisherman's Wharf and the baseball stadium.

There are ferries, but they only go from a very few points in SF to a very few points in Alameda, Oakland, and the north bay.

Seems like most of the time, the places you're trying to get to aren't close to the water anyway.