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Gov. Andrew Cuomo is responsible for the MTA, which oversees the city's subways, and is also co-chairman of the Port Authority, which covers the World Trade Center site and PATH trains to New Jersey.

"The subway tunnels, some will be like this, some will actually be worse," he said. "The subway tunnels, the design of the city was premised on the fact that the water doesn't come over the banks."

Lower Manhattan flooded from three different points: the Hudson River to the west, the harbor to the south and the East River near South Street Seaport. While streets like West Street were five feet deep in water Monday night, eventually, that water receded, although it seemed to end up underground.

Officials haven't even started the long process of pumping out water from the Hugh L. Carey (Brooklyn Battery) Tunnel, which MTA Chairman Joseph Lhota said was filled with 43 million gallons of water.

"We're just assessing the situation now and we have teams being flown in from across the country, equipment being brought in from across the country," Cuomo said. "Because there is a lot of water, as you can see."

The Obama Administration is making some of the nation's experts on flood cleanup available to New York. They include members of Army Corps of Engineers, who were in New Orleans in the aftermath of Hurricane Katrina.

"Well, we saw flooding in Katrina," said Col. Paul Owen of the Army Corps of Engineers. "Flooding in Katrina was different, though, because it was surface water. This is sub-surface water.

Gov. Cuomo was asked how long it will be before all this water is pumped out. He said it will likely be more than a few days but not a few weeks. They are just now assessing what needs to be done to get the water out of the tunnels.