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No, there aren't any whirlpools in Emerald. Its basically useless if you ask me. You need the move in HG/SS though.
You need the HM whirlpool.
First you must have a badge from the Mahogany Town gym leader (he uses ice types). Next you must find the HM Whirlpool. Equip Whirlpool to a Pokemon and go to one of the Whirl Islands and use the move Whirlpool on a whirlpool.
In Ruby (what I have), Wailmer learns it. However, it's practically useless due to the fact that there aren't any whirlpools in Ruby, Saphire, or Emerald. So it is only a move, NOT a HM.
you need a Pokemon that can use HM move whirlpool