The view from the balcony showed water reaching almost to the top of the fire truck used by Engine Company 21 to respond to the attack in 2001, and the truck on which Ladder Company 3 arrived. A Fire Department ambulance was also surrounded with water. All three had been shrink-wrapped in plastic before they were installed in the museum. With the floodwaters still standing, there was no way on Friday to assess how much additional damage the already battered vehicles had sustained, or whether the plastic enclosure had protected them.

The archipelago of partly submerged artifacts includes the last column of the original twin towers. This 58-ton piece, more than 36 feet high, was removed with funereal ceremony in May 2002 to symbolize the end of the first phase of recovery, the clearance of the World Trade Center site. It was then stored in a climate-controlled area of Hangar 17 at Kennedy International Airport while undergoing conservation. It is still in a climate-controlled enclosure, so its condition has not been assessed. Many of the personal effects that had been taped to the column were removed long ago for safekeeping. But the column is also covered in spray-painted graffiti from first responders, rescuers and recovery workers.

The last column, the steel cross, the damaged vehicles and the so-called survivors’ stairway were all hoisted down into the subterranean museum during the early phases of construction. They could not have been moved in after the completion of the memorial plaza, which doubles as the museum rooftop.

Mr. Daniels said Friday that the pumping out of the museum was “fully under way,” but that it was too early to say when construction might resume or, for that matter, when the Sept. 11 memorial might reopen to visitors.