Heavy rainfall pounded New York City and the surrounding region Friday morning, leading to reports of flash flooding throughout the area and disrupting service on major subway lines and stranding some morning commuters.

The National Weather Service issued a flash-flood warning for Manhattan, Brooklyn and Queens that was set to last through 12:30 p.m. Additional warnings were in effect for the Bronx, Staten Island and Jersey City, N.J. The Weather Service warned that flash flooding would affect highways, streets and underpasses.

Video showed cars driving through flooded roads in parts of Queens and Brooklyn. The area around Kennedy International Airport, in Queens, had reported more than 3 inches of rain. At La Guardia, travelers were told to avoid the area around Terminal A, which was closed.

Officials cautioned New Yorkers to stay off the roadways and avoid traveling.

“This water is deadly,” Gov. Kathy Hochul said in an interview Friday morning with NY1. “That is our message for New Yorkers. Don’t take this for granted.”

Mayor Eric Adams’s office sent a travel advisory via email Thursday evening at 11 p.m. and posted updates on Twitter. He was scheduled to hold a news conference with the governor at 11 a.m.

The Metropolitan Transportation Authority warned of “major disruptions” to subway service, especially in areas of Brooklyn, because of flooding. There was no 2, 3, 4 or 5 train service in Brooklyn, northbound N trains were delayed and B train service was suspended in both directions.

A crowd stood outside the Clark Street station in Brooklyn Heights at 9 a.m. unsure of how to proceed. Tracks were flooded at the stop that sits at one of the deepest underground points in the subway system and leads passengers under the East River to Manhattan.

Optimists headed to the A train stop at High Street, a few blocks away, where trains were meant to be running. But there were major delays and at one point an announcer inexplicably advised passengers, most of whom were headed to Manhattan, to consider taking the Long Island Railroad.

Blocks away, as water swept downhill, one girl huddled close to a companion, scolding herself for leaving her rain gear at home. A teenage boy ducked out of the way of a younger peer’s pink unicorn umbrella, which threatened to stab him on the face.

On Manhattan’s Upper East Side, floodwaters spilled onto the sidewalks. Many people tried to brave the morning commute, bundling children into rain jackets and sprinting toward the Q station on the corner of 83rd Street and Second Avenue in water-logged shoes. Undeterred by the heavy rain, one man squelched down a flooded sidewalk for his morning run.

By 9:30 a.m., all lanes of the Belt Parkway were closed in both directions at Cropsey Avenue in Brooklyn because of flooding and parts of the F.D.R. Drive were experiencing delays.

The rain is expected to continue throughout the day, with several more inches expected through the evening, said Joe Pollina, a meteorologist with the National Weather Service.

“We still have to see what the afternoon brings,” Mr. Pollina said.

Claire Fahy, Mihir Zaveri, Jonah E. Bromwich, Emma Fitzsimmons, Luis Ferré-Sadurní, Judson Jones, Patrick McGeehan and Ginia Bellafante contributed reporting.