Superstorm Sandy flooded parts of the New York City subway system, rail yards and bus depots, creating what officials are calling the biggest disaster of its 108 years in existence.

"The New York City subway system…has never faced a disaster as devastating as what we experienced last night," MTA Chairman Joe Lhota said in a statement. "Hurricane Sandy wreaked havoc on our entire transportation system, in every borough and county of the region."

In addition to flooding in a handful of tunnels and bus garages, Lhota said a portion of the Hudson line on the Metro-North Railroad had lost power.

"We are assessing the extent of the damage and beginning the process of recovery," he said. A time frame for when one of the world's largest public transportation networks would be back up and running was not yet available.

Hurricane Sandy: Full Coverage

The subway system, which averaged 5.2 million weekly riders last year, was preemptively shut down Sunday evening.

Gov. Andrew Cuomo said he hoped the closure would keep New York-area residents from being "up and about."

"[Trains are] not intended to be submerged," he said. "And we want people to stay at home."

The city is planning on an aggressive bus strategy during subway repairs. It may include limiting or shutting lanes for private vehicles in order to help expedite bus traffic.

Mass transit was also preemptively shut down in Boston, Philadelphia and Washington D.C.

ABC News' Richard Esposito contributed to this report.