Hurricane Henri kept on track to wreak havoc on New York early Sunday — but early downpours had already sparked major flooding in the Big Apple by Saturday night, shuttering subways and inundating roadways.

The tempest was on course to make landfall on Long Island or in southern New England by midday Sunday, according to the National Oceanic and Atmospheric Administration.

But storms caused in part by moisture from Henri hit the region late Saturday bringing heavy rains and flash floods to New York City, and even forcing drivers out of their cars in Brooklyn.

Photos captured by The Post in Gowanus showed police and firefighters assisting drivers whose cars appeared to be completely stuck in more than six inches of water.

Twitter users also reported flooding in Williamsburg, as drivers navigated streets-turned-rivers by the earlier than expected rains. The deluge, along with lightning, brought the star-studded We Love NYC Homecoming concert in Central Park to a halt at around 7:30 p.m. The highly anticipated event was officially canceled about two hours later.

Close to 4 inches of rain came down over Central Park on Saturday night, with 1.69 inches falling just between 10 p.m. and 11 p.m., the National Weather Service said.

Water even made it into some subway stations. Subway officials were forced to suspend 1 trains between 14th Street and 96th Street and 3 trains between Harlem-148th Street and Penn Station shortly before midnight due to track flooding near 79th Street, the MTA said. Riders were advised to take the 4 train or the 2 train, which was rerouted onto the east side.

One tweet showed a waterfall pouring down on the tracks in Queens as the A train waited with its doors open.

Another showed even more torrential floods spewing onto the G line platform at 23rd Street in Queens as straphangers waited for the train.

An MTA rep confirmed “a water condition” at 79th Street. Service was completely out between 34th Street and 79th Street, the rep said.

“This is why I avoid the MTA like the plague, like COVID, and try to walk,” said Emily Kay, 25, who was trying to get home to Harlem shortly before 2 a.m. from the 79th Street station, where a 1 train was stopped on the track as emergency transit workers worked to fix the situation.

Pools of water flooded the path next to the platform.

“This is not convenient. We’re stuck here staring at a subway,” she said.

A trains were also running express between Hoyt – Schermerhorn Street and Euclid Avenue in Brooklyn due to flooding at the Utica Avenue station.

Even more flooding is expected when Henri comes crashing into the region as a Category 1 hurricane or a strong tropical storm.

It is expected to dump up to half a foot of rain across the Northeast, with storm surges expected along the coast of eastern Queens and Long Island, the National Hurricane Center said.

All of New York City was under a tropical storm warning as of 11 p.m. Saturday, meteorologists said. Trains and flights were already being canceled ahead of the tempest.

Hurricane conditions were expected on Long Island and from New Haven to just east of the Rhode Island-Massachusetts border.

Reports from nearby Air Force aircraft indicated Henri was moving at 21 miles per hour in the northwest direction — with winds near 75 miles per hour and gusts even faster.

Parts of New York City, northern New Jersey, Long Island and New England could see three to six inches of rain, the NHC said. Isolated areas could see as many as 10 inches.

Henri is expected to wallop Connecticut, Rhode Island and the southernmost part of Massachusetts after it passes through the New York region.