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The Seaweed Sanctum is an area in Jolly Roger's Lagoon in Banjo-Tooie. It is found in Atlantis.
This area is where the Whirlweeds live and leads up to the area in which the Big Fish can be found and access to freeing Merry Maggie Malpass. A Jinjo can also be found here as well.
Though the room contains many Whirlweeds, only a few will actually attack the player. These are chosen at random when the player starts a new game.