I don't find a discrete definition of the expression, but in general, "to ship X" is to take X on board. I agree that "to ship water" is understood to be an undesirable state of affairs. It's not used for intentional things like "taking on ballast," or for putting in a supply of drinking water.
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According to this page, to "ship" an item means to take it inboard, so "shipping water" means taking water in over the bow.
http://www.photographers1.com/Sailing/NauticalTerms&Nomenclature.html
Corroborated by this page, which claims that the flared bow of a ship
The OED shows "ship a sea" (esp.) as a phrase in its earliest citations, starting in 1698, meaning to have a wave break over the ship. They do not go so far as to say that more recent uses are extensions of that phrase, but that does seem to be the case. This use of "ship" is no mystery. The vessel takes a wave on board.
anonymous'shipping water'
This appears to be jargon. It is not familiar to all English speakers and is not in general use outside nautical contexts.