Powerful thunderstorms brought torrential rain and flash flooding to Long Island early Monday, forcing multiple rescues and briefly closing parts of major highways leading to New York City. The National Weather Service issued a rare flash flood emergency during the worst part of the storm, describing it as a “particularly dangerous situation.”

The same storm system dumped nearly 10 inches of rain in some areas of Connecticut on Sunday, causing rivers to crest their banks and leading to another flash flood emergency declaration and about 100 evacuations, officials said. And in New York City, the downpour disrupted trains and forced the authorities to ground or cancel flights.

On Monday, more than 900,000 people in Suffolk County on Long Island were under a flash flood emergency that expired before dawn, according to the National Weather Service. A flash flood emergency is the highest level of flood warning.

Brian Ciemnecki, a meteorologist with the Weather Service in New York, said that it was rare to issue such an alert for the area and that weather officials made the call after receiving numerous reports of water rescues and other damage caused by the storm.

The rain in most parts of Long Island had stopped by early Monday, he said, but issues were expected to carry over into the morning commute.

“If you’re traveling, I would expect, probably encounter some potential road closures just in the residual, leftover, flooding that occurred, especially in the northern half of the island,” Mr. Ciemnecki said.