Federal forecasters issued flood alerts for 39 million people late Saturday into Sunday as a line of thunderstorms developed from Washington, D.C., to New Haven, Connecticut.

New York City Emergency Management warned residents of heavy rain and possible flash flooding into Sunday morning as the city opened 51 weather shelters for those vulnerable to floodwaters, including people in basement apartments.

The National Weather Service issued a slew of flood alerts, including flood watches, late Saturday through early Sunday for parts of Maryland, Pennsylvania, Delaware and New Jersey.

A flood watch for Washington, D.C., expired at 1 a.m. Sunday.

Philadelphia and neighboring counties were under a flood watch through morning. A flood watch for New York City was scheduled to start at 4 a.m. Sunday and extend through noon.

New York City Emergency Management said in a statement that 5 to 7 inches of rain could fall in Nassau and Suffolk counties, as well as in southern Connecticut, and warned that the city’s eastern boroughs could also be hit with heavy rain.

“A small shift in where the rain sets up would bring 5 to 7 inch totals and a much higher flash flooding risk into eastern Brooklyn and Queens,” it said. “New Yorkers in those neighborhoods living in basements and below grade are urged to move to higher ground tonight.”

A flood watch for parts of southern Connecticut, including northern New Haven, was in effect through Sunday afternoon, according to the weather service.

The thunderstorms are emerging as a trough of cold air high in the atmosphere moves east and clashes with warmer air, federal forecasters said.

“The combination of instability, deep moisture, and forcing, may lead to an elevated threat for excessive rainfall and severe thunderstorms,” the weather service said in a forecast discussion late Saturday.