What Pokémon makes the Whirlpool in Pokémon Crystal?

Answer

In most of Johto and Kanto in Pokemon Crystal, whirlpools naturally occur in the water. No one Pokemon is responsible for the general amount of whilpools in Pokemon Crystal, and they simply serve as game features which obstruct your path until you have enough experience to pass them.

However, the whirlpools surrounding Whirl Island are most likely to be caused by Lugia, who resides deep within the Island. Lugia lives in the ocean and is rumoured to have the ability to create whirlpools even when it moves.