[Parker]

     I know it sounds too sci-fi and anime-ish, but instead of the usual arcologies, I've been experimenting with shallow underwater corporate facilities in my game.   
While I admit the allure of having toxic sea spirits and Awakened sea creatures (with a dash of 'Call of Cthulhu' style) acting as threats to my players as well as your typical corp/military stereotypical threat adds spice to the run; I like being creative.  Heck, I admit I'm not above stealing ideas from TV, movies, and books.  As long as my players enjoy themselves, that's what important.

[Wakshaani]

There are several underwater facilities in Shadowrun, as well as floating Arcologies (Arkobloks) that can trundle around at sea.

Check out Hazard Pay for more on this.

[Xzylvador]

Corporate Guide talks about them as well. AFB ATM, but one of the more powerful AA's, Proteus (I think?) kind of specializes in them (amongst other things).

[Ener]

Also the example used in the system design in unwired is an underwater kelp farming and research facility (though obviously this focuses more on it's matrix structure than the actual facility)

[Zunimancer]

In Runner Heavens it has a short describtion on EVOs Xuan Wu Aquacology. Was mentioned also in the "Hong Kong Tourist Brochure" in New Dawn.

Arsenal tells us "... or the growing number of aquacologies.