(nautical) In that part of a ship's side or bottom which is frequently brought above water by the rolling of the ship, or fluctuation of the water's surface.
(colloquial, by extension) At the vulnerable part or point of anything.
(colloquial, euphemistic, by extension) At a person's crotch (i.e. between the sources of flatulence and urine).
Source: en.wiktionary.org