The region was hit with heavy rain Monday evening, resulting in flash floods that not only impacted roads and air travel, but also the transit system.

A flash flood warning was in effect in New York City until 9:45 p.m., and New Jersey Gov. Phil Murphy declared a state of emergency. Middlesex, Morris and Somerset counties remained under a flood warning until 7:15 a.m. Tuesday.

New Jersey's governor declared a state of emergency after heavy rains pounded the Northeast. New York City also warned residents of basement apartments to prepare for possible evacuations.

When the train doors opened, "quite a lot of water came in, so almost all of us stood up on the seats," a passenger told Newsweek.

The subway system, which is more than a century old, is relied on by millions of passengers every day and weaves the city into a cohesive network.

Roads and streets, meanwhile, are likely to flood during the downpour, said the Office of Emergency Management’s advisory. Flooded roads could spell trouble for the city’s bus riders and drivers. The city warned motorists not to drive through flooded roads.

Central Texas is facing the threat of more flooding as persistent storms bring heavy rain to the area, while a separate system will unleash downpours on New York City and throughout the Mid-Atlantic.

Another round of showers and thunderstorms moved across the Mid-Atlantic Tuesday after intense rain set off dangerous flash flooding from Virginia to New York on Monday, leaving at least two dead and prompting dozens of rescues as water overwhelmed roads and subways.