Jolly Rogers Lagoon and Atlantis in Banjo Tooie are much more memorable than Mario 64's levels, IMO.
Still, my favorite would have to be Amiss Abyss from DKC: TF (many other DKC levels, too). ALso that boss in Shadow of the Colossus; it was great and very doable for a water-based area. Also, Undersea Palace in Crono Trigger, though that doesn't really count. It does have the best music ever, though
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