The heaviest rain from a widespread storm that drenched the eastern United States appeared to have ended in much of the Mid-Atlantic and Northeast by Wednesday morning, but meteorologists said the risk of flooding had just begun.

“The worst time for flooding is right after the rain stops,” said Patrick Wilson, a meteorologist at the National Weather Service office in Blacksburg, Va., in a region of the state where heavy rain closed roads on Tuesday. “It takes time for all the water to drain down.”

After the storm wrung out the moisture it had gathered from the Gulf of Mexico, rain began trickling down mountains into creeks, accumulating in tributaries and streams, from which it can eventually flood rivers, he said.

Flood warnings, indicating that flooding was imminent or had been reported along a river, applied to millions of people early Wednesday in much of Virginia and parts of Connecticut, Delaware, Massachusetts, New Jersey, New York, Pennsylvania, West Virginia, North Carolina and parts of several other southern states, according to the National Weather Service.

Many of those warnings were expected to last until late Wednesday morning, but forecasters said the floods could last through Thursday.

Coastal flood warnings were also in effect in large cities along the East Coast, including Baltimore, New York, Philadelphia and Washington.

Officials echoed meteorologists’ warnings. Gov. Kathy Hochul of New York said on Tuesday evening that she was concerned about the threat of flooding in her state, especially in the Hudson Valley, where a rainstorm had killed one person over the summer.

In Annapolis, Md., where parts of downtown were submerged on Tuesday night, emergency officials said that the flooding was expected to rise by an additional foot by the high tide around 3 a.m. Wednesday. The authorities in nearby Baltimore issued a similar warning.

In the Appalachian region, the storm dropped more than three inches of rain on Tuesday, triggering flood warnings throughout central Virginia, said Mr. Wilson, of the National Weather Service. By early Wednesday, roads near creeks, streams and low-lying areas were flooded. He said he expected the swell to reach population centers, like the town of South Boston, within hours.

Mr. Wilson said that residents should be careful when driving. “The number one risk of danger during flooding is driving on flooded roads,” he said. “That’s why you hear, ‘Turn around, don’t drown.’”

The threats to America’s aging flood infrastructure are growing because of climate change. Researchers say that climate change is intensifying rainstorms — warmer air can hold more moisture. So storms are expected to deliver more rain than local pipes and culverts are designed to handle.