New York ? A torrential downpour sent water surging through New York’s subway system and highway tunnels and across airport runways Wednesday, leaving thousands of commuters stranded and one big question: How could 3 inches of rain bring the nation’s largest mass transit system to a halt?

The storm, which also spawned a rare tornado, hit just before dawn. By rush hour, the subway system was virtually paralyzed when pumping stations became overwhelmed. Bedlam resulted from too much rain, too fast; some suburban commuters spent a half day just getting to work.

“One big rain and it all falls apart,” said Ruby Russell, 64, as she sat waiting on a train in Brooklyn. 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 sort of delay as track beds turned into streams gurgling with millions of gallons of rainwater. The washout was the third time in seven months the subways were disrupted by rain.

The National Weather Service said a tornado touched down in Brooklyn, where winds up to 135 mph 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.

“It’s a once-in-a-lifetime event,” said Jeffrey Tongue, a Weather Service meteorologist.