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The Aquaboy and Aquagirl perks allow you to breathe underwater, remove radiation damage while swimming, and may even make you undetectable while submerged.”— Fallout 4 loading screen hints
With the first rank of the Aquaboy perk, the player character no longer takes radiation damage when swimming, and gains the ability to breathe underwater. The second rank of the perk allows the player character to submerge themselves completely in a body of water to disappear from sight completely, handy for losing hostile opponents.