Maybe this isn't what you mean, but the lighter colored water on the map with something like waves drawn on it is part of the land biome and will change what's displayed on the HUD. For the swamp, and I'd have to double check, I don't believe it draws the wavy bit on the map. The wavy parts seem to be, like you said, part of some other biome that the swamp is slapped on top of.

The ugly black parts on the map are also used where water is, if I recall, and sailing into that should change it to "Swamp." It tends to be pretty shallow and full of leeches, so I never pull up that close in a swamp.