After days of sitting under a blanket of wildfire smoke, the Northeast on Saturday was being hit by thunderstorms that were flushing out the acrid air but also threatening the area with strong winds and heavy flooding rains.

Forecasters for the National Weather Service warned of winds over 70 miles per hour as well as a small chance for tornadoes in an area that spread from Baltimore to New York City.

These storms were also bringing a chance for scattered heavy rain that could lead to flash flooding across the Ohio Valley into the Mid-Atlantic and southern New England, with New York City, Newark and Philadelphia among the cities with a particularly high risk.

Flood watches and severe thunderstorm watches were in effect across parts of the Mid-Atlantic, and forecasters said people could keep an eye out for more urgent warnings. While a watch is a heads-up that conditions are favorable for hazardous weather, a warning is an order to take immediate action.

Clusters of thunderstorms formed Saturday morning into the early afternoon from the lower Great Lakes into the Mid-Atlantic. Rain pounded New York City in the early afternoon, and the National Weather Service issued a flash flood warning for Manhattan, Brooklyn, Queens and surrounding areas.

“The worst of it is in Brooklyn and Queens, where we got over two inches of rain,” said Bill Goodman, a meteorologist with the Weather Service office in Upton, N.Y.

This was the first round of storm activity. A second, more intense line of thunderstorms was expected to move across the region later Saturday afternoon into the evening.

The area just north of Baltimore to New York City was likely to see the most severe storms, said Brian Hurley, a meteorologist with the Weather Prediction Center. Some of these storms could bring damaging winds to some areas, but not all of these areas will be hit by the strongest winds.

Mr. Hurley said it was difficult to pinpoint exactly where the most hazardous weather would occur. Thunderstorms are tricky to forecast, and they can suddenly form, darkening clear skies and bringing heavy bursts of rain, strong winds and lightning.

Mr. Goodman said it was unclear what the evening storms would bring to New York City.

“With this second round we’re going to have to wait and see what happens,” he said.