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No, water breathing is a fun perk, especially when you're fishing for salmon. But I haven't found any truly useful applications for it. There's no need to swim underwater anywhere (a couple of partially submerged ships don't count; it's only worth taking an Argonian just to open a chest and get 50 coins, and that's a pain). Even on the surface, it's not always necessary (but sometimes it's nice to have, of course, to clear out enemies, but you don't need water breathing for that).