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.
A well deck is an exposed deck (weather deck) lower than decks fore and aft. In particular, it is one enclosed by bulwarks limiting flow of water and thus drainage so that design requirements are specific about drainage and maintenance of such drainage with that definition applying even to small vessels. The United States Coast Guard, Sector Upper Mississippi River, Small Passenger Vessel Information Package notes:
""Well deck" means a weather deck fitted with solid bulwarks that impede the drainage of water over the sides or an exposed recess in the weather deck extending 1/2 or more of the length of the vessel over the weather deck".
Explicit requirements exist for drainage requirements on ships with well decks. On many vessels the cargo hatches and cargo handling booms and winches were located on the well decks between a central superstructure and raised forecastle and poop.
Naval vessels into the World War II era often had well decks between stacks with the space sometimes reserved for aircraft and catapults as seen in the photograph of the USS Indianapolis's well deck (note ladders down into the well deck from surrounding decks).
In commercial ship design categories, the "well deck ship" type the profile of the main deck line is broken rather than being flush or unbroken from bow to stern. The earliest cargo steamers were flush deck with openings below rimmed only with low casings. Later designs eliminated this design as dangerous with bulwarks and eventual evolution into the "three island" design with raised forecastle, central bridge and poop superstructures and well decks between.
The well decks of passenger liners were often for the lowest class passengers' use with the well deck of the Titanic reserved for third class passengers. By mid 20th Century the concept of well deck design in passenger liners was "old fashioned" and newer ships were designed with flush decks.