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You can't walk underwater like in Ocarina of Time, but the Iron Boots are a handy addition nevertheless. Equip them and Link will become very heavy. This means that Link won't be able to move around quickly, but the added weight is necessary for a number of puzzles and situations. There are plenty such puzzles in the game -- and thankfully, you can equip the boots just like any other item, so you don't need to access the menu every time like in Ocarina of Time.