Wiktionary
n. (context nautical English) A sunken deck between the forecastle and the poop
Wikipedia
In traditional nautical use, well decks were decks lower than decks fore and aft, usually at the main deck level, so that breaks appear in the main deck profile, as opposed to a flush deck profile. The term goes back to the days of sail. Late-20th-Century commercial and military amphibious ships have applied the term to an entirely different type of hangar-like structure, evolving from exaggerated deep "well decks" of World War II amphibious vessels, that can be flooded for lighters or landing craft.
Usage examples of "well deck".
In the harsh glare of the searchlights she seemed more forlorn, more abandoned than ever, so deep now by the head that the f or'ard well deck had vanished, and the fo'c'sle, like some lonely rock, now awash, now buried deep as the big seas rolled it under -- the wind had gone, the rain had gone, but the seas were almost as high as ever, and even more confused.
He came to the aft end of the superstructure, where an iron-railed and iron-runged companionway led down to the well deck, then up another similar stairway to the small poop deck where an emergency hand steering wheel and the 3-inch gun were located.
It has a hell of a high stern, like an amphib, but there doesn't seem to be any well deck.
Brim surfaced just in time to see Barbousse knocking gently from the well deck.
The colonel's words were already spreading among the Marines crowded in the LCAC's well deck.
Underneath the flight deck that you aviators think so much about, there's something called a well deck--it's open to the ocean, and it's where we keep all of our amphibious vehicles.
Murdock replied, taking the SCUBA and stowing it in the Boghammer's aft well deck.