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NEW YORK — The subway system ground to a halt Wednesday night as rain flooded into the transit system.

Even on a normal day, the MTA pumps 14 million gallons of water from subway stations, so days with heavy rain pose challenges. The subway system is shallow in most places, MTA Acting Chair Janno Lieber said.

“The subway system is not a submarine,” he said. “You have the utilities and other activities at the street level that have poked holes in the subway’s roof.”

Of the MTA’s 665 miles of subway track, 418 are underground, which means they’re vulnerable to flooding.

Flooding issues below ground are often caused by issues at ground level, he explained. When the drainage and sewer system are overwhelmed, it sends water flooding into the subway system.

As part of a subway action plan, the MTA cleared debris from over 40,000 street grates in recent years. The grates are needed for ventilation, but there’s often buildup of garbage and leaves in them.

“That is very hard to prevent,” Lieber said