One driver captured video of a road underwater in Wayne, New Jersey.
Heavy downpours in North Jersey forced Amtrak to temporarily suspend rail traffic between New York and Philadelphia.
Officials said it was due to flooding conditions in Newark around 8:20 p.m.
"I'm devastated. They keep changing the update," said Marcia Roye, who planned to travel to Maryland from the 30th Street Station in Philadelphia. "I'm going to wait it out, and hopefully I'll get there at some point."
Amtrak announced service was restored between 30th Street Station and New York Penn Station around 10:30 p.m.
In Bethany Beach, Delaware, storms caused major flooding and road closures.
State police said Route 1 northbound at the Indian River Inlet Bridge was closed to traffic at Fred Hudson Road due to flooding on the north side of the bridge.
Police advised drivers to find an alternate route until the road was cleared.
Beachgoers warned after over a dozen rescues made at Jersey Shore amid stormy weather
In Ocean City, New Jersey, the beach closed when thunder and lightning rolled through.
Officials with Ocean City Beach Patrol said there were at least five major rescues in the water due to the intense waves and swimmers who were out of sight.
In Ventnor City, beach patrol leaders said waves were rough there as well, with most reaching five to six feet high.
Lifeguards there made 17 rescues on Sunday, authorities said. A rip current warning is in effect at the Jersey Shore until Tuesday.