All it took was about three inches of rain in three hours to bring the nation's largest mass transit system to its knees.

Subways tracks were swamped, buses were overwhelmed and commuter trains were held up for hours because of flooded tracks. Some roads became waterways, and one woman was killed in car accident during the storm.

While much of the mess had been mopped up by early Thursday, Wednesday's deadly deluge — the product of a storm that also spawned a rare tornado — left many commuters angry. As the region faced the possibility of more storms within a day, Gov. Eliot Spitzer called for fixes for what has become chronic subway flooding.

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Forecasters saw "the potential" for a new round of heavy thunderstorms in the metro area Thursday night or Friday morning, National Weather Service meteorologist Adrienne Leptich said. She said it was impossible early Thursday to be certain where the storms might strike, or how severe they might be.

Wednesday's storm hit just before dawn. By rush hour, pumping stations became overwhelmed, and the subway system was virtually paralyzed. Bedlam resulted from too much rain, too fast; some suburban commuters spent a half day just getting to work. Crews worked feverishly to pump out the subways, but it took until the evening rush hour to get most of the system back on line.

"One big rain, and it all falls apart," Ruby Russell, 64, said as she sat waiting on a train in Brooklyn around 9 a.m. Wednesday. She had been trying to get to Manhattan for three hours.

The failure renewed a debate about whether the network of pumps, sewers and drains that protects the city's subways from flooding needs an overhaul. Every line experienced some measure of delay as track beds turned into streams gurgling with millions of gallons of rainwater. The washout marked the third time in seven months that the subways were disrupted by rain.

Metropolitan Transportation Authority engineers were asked to report back to Spitzer within 30 days with suggestions about how to deal with the flooding.

"We have a design issue that we need to think about," Spitzer said.

The National Weather Service said a tropical air mass dumped an extraordinary amount of rain in a short period of time. The worst was recorded between 5 a.m. and 8 a.m., with 2.5 inches falling on Central Park and almost 3.5 on Kennedy International Airport.

At one point, more than 1.5 inches fell within an hour in Central Park, Leptich said.

Naturally, the stormwater sought the low ground, and that meant the subways. Water poured in through vents, drowned the signal system and flooded the third rail, forcing a shut-off of power on some lines.

MTA Executive Director Elliot G. Sander said the intensity of the rain was simply overwhelming. The subway's drainage system can generally handle a maximum of 1.5 inches of rainfall per hour; on an average day, hundreds of MTA pumps remove 13 million gallons of water from the system, which includes several tunnels and stations below sea level.

Public officials called for improvements in the drainage system after a similar rain-related shutdown in 1999, and the MTA made some changes after another round of paralyzing tunnel floods in 2004, when the remnants of Hurricane Frances washed out the subways for hours.

The latest subway problems come as weather experts predict New York is due for a major hurricane. A storm with 130 mph winds and a 30-foot storm surge could cause the Hudson and East rivers to overflow — and bring with it far more significant flooding than a severe rainstorm.

The city's 19th-century sewer system, which doubles as a storm drain, can handle steady rain, "but when it comes to these very intense, high inch-count rain events, over a short period of time, it is very difficult," said Michael Saucier, a spokesman for the city's Department of Environmental Protection.

DEP Commissioner Emily Lloyd said the city is spending $300 million per year upgrading its piping systems and has been gradually building a more robust stormwater drainage system to replace the old combined sewers that handled wastewater and rain.

In Manhattan, Times Square was one huge mess Wednesday, packed with many of the 4 million riders who rely on the subway system daily. Thousands waited for hours for any means of transportation, jostling one another to get on the few buses that arrived. The suburbs were no better: In Westchester County, hundreds of commuters were stopped on a Metro-North train due to track flooding.

Streams of people in business attire — with briefcases, cell phones and BlackBerries in hand — trudged through drenched streets toward the subway. But it, too, was flooded. The hordes then made a beeline for buses they'd spotted up the street.

The storm was blamed for at least one death. A woman on Staten Island died when a car got stuck in an underpass and another car came along and hit hers, Mayor Michael Bloomberg said. A handful of people were injured, Bloomberg said.

The National Weather Service said a tornado touched down several times in Staten Island and in Brooklyn, where winds downed trees, tore off rooftops and wrapped signs around posts. At least 40 homes were damaged.

Tornadoes have hit New York City before, but not often. The National Weather Service had records of at least five, plus sketchy detail on the last reported tornado sighting in Brooklyn, in 1889. None was as strong as Wednesday's twister, which had winds as high as 135 mph.

"It's a once-in-a-lifetime event," said Jeffrey Tongue, a Weather Service meteorologist.

Lanie Mastellone, who lives in Brooklyn's Bay Ridge neighborhood, awoke as her roof was coming off. Before escaping, she ran to get her late husband's wedding ring.

"It happened so quick. Maybe he was watching over me," Mastellone said.

The weather also created problems for the region's airports, where delays of up to an hour were reported, and thousands of people throughout the region lost electricity for part of the day.

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