At the 157th Street subway station in Washington Heights, water pooled around the entrance and inside, passengers trudged through deep water that has seeped into the system.
Service on the A train line were suspended between 207th Street in Inwood and 181st Street because of an excessive amount of rainfall at track level.
B trains were also delayed entering and leaving Bedford Park Boulevard as a result of flooding.
Crews spent the night pumping stations across the system. Sometimes, it didn't even take long.
In Mona Jenkins' ground floor apartment in Washington Heights, the water came in torrents -- at least a foot high at one point.
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During an 8:30 p.m. press conference, MTA Interim President Sarah Feinberg said Upper Manhattan and the Bronx took a beating from the heavy downpours.
"The 1 line and A line took a beating, tons of station flooding," Feinberg said.
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Eyewitness News interviewed New York City Transit Head of Subways Demetrius Crichlow, who said the city is prepared to tackle any challenges due to the storms and Elsa.
"We're doing pretty well, we prepped a lot for this in advance, we have people in place to address this," Crichlow said.
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Feinberg said she hopes the impact from Elsa will be spread out over a longer period so the drains in the subway can handle it better.
Like Feinberg, Crichlow urged residents to stay safe and only commute if absolutely necessary Friday morning.
"We'd like to just encourage people to remain safe out there, we're not going to put any of our customers in danger so we expect to resume service when we feel it's safe to do so," Crichlow said.
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