Dolphins and sea lions are actually termed Marine Mammal Systems Mk. 4 and Mk. 7 by the U.S. Navy. As was said before, they serve both mine countermeasure and harbor security roles. They've been in use, more or less, since the 1970's.
I did some research on them as part of a paper this past semester. In mine countermeasure operations, they'll swim alongside a small craft (usually a zodiac) and tap a small paddle each time they find a mine. They'll then be given an acoustic marker to place on the mine. As was said before, they're pretty much the only method we have of reliably finding buried mines.
To get from place to place, they'll actually be air-lifted on C-5's in huge saltwater swimming pools. Once on station, they'll be kept in larger specially-built tanks aboart a landing vessel, or something else with a well deck.
The one that "swam away" during the Iraq conflict was actually thought to have been attacked by marine mammals native to the area, sort of a territorial dispute.
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