Brattleboro, Vermont (CNN) -- Dangerous, damaging flood waters emerged Sunday night as one of the biggest threats from Irene, which impacted millions with its strong winds and drenching rains over its three-day run up the East Coast.
The storm, which was a hurricane for days before weakening to tropical storm status early Sunday, was blamed for at least 20 deaths across eight states. The U.S. government estimated that the cost from wind damage alone is expected to top $1 billion, with downed power lines leaving more than 4 million people without electricity.
"I want people to understand that this is not over," President Barack Obama said Sunday evening from Washington. "The impacts of this storm will be felt for some time, and the recovery effort will last for weeks or longer."
The storm that first hit the U.S. mainland in North Carolina Saturday morning as a Category 1 hurricane was no longer even a tropical storm as of 11 p.m. Sunday, the National Hurricane Center said. By then, it was 50 miles north of Berlin, New Hampshire -- near the Canadian border -- with maximum sustained winds of 50 mph.
Some of the biggest, continuing headaches involved flooding, as tidal storm surges and overflowing, fast-moving rivers left homes in North Carolina and points northward awash. Flood warnings and watches were in effect Sunday night for much of New Jersey, Pennsylvania, eastern New York, Connecticut, Massachusetts, Vermont, New Hampshire and Maine.
Numerous "swift-water" rescue teams were dispatched Sunday night around Vermont, where state emergency management spokesman Mark Bosma said some small towns were "entirely covered with water" and people, including a woman who was in labor, were stranded in schools and cars.
Vermont State Police Capt. Ray Keefe said Wilmington is "cut off," hundreds of roads had been closed, and some homes were washed off foundations and into lakes.
And "conditions continue to worsen dramatically" in Vermont's capital of Montpelier, city manager William Fraser said Sunday night, noting National Weather Service warnings of rising river waters that have spurred evacuations and will cause "major flooding" downtown early Monday morning.
"The conditions today have been awful," Bosma said. "Water is pretty much everywhere."
Also hard-hit was New Jersey, where initial fears about coastal flooding -- which had prompted the evacuation of more than 1 million people from the shore -- had given way to fresh concerns about inland flooding.
That left many residents like Guy Pascarello, whose family's Secaucus home of 40 years was declared uninhabitable after it became inundated by three-foot-high waters, trying to figure out what to do next.
"I don't know (what we'll do), this is all new ground," Pascarello said. "The good news is that it's just stuff. This is a home and we love our home, but it's just things."
Even locations well inland, like Princeton Junction about halfway between New York City and Princeton, had waters as high as 12 feet that covered roads and bridges, resident Edward Picco said. And streets in downtown Millburn saw major flooding when the Rahway River overflowed early Sunday morning, said Lt. Peter Eakley, the town's deputy emergency management coordinator.
"It's crazy. ... The water is moving between buildings, up, down, all sorts of different directions," Rich Graessle said from Millburn.
Along the shore in Long Beach, New York, water poured underneath the boardwalk and into the city's downtown.
Outside Philadelphia, meanwhile, waters climbed to street-sign levels in Darby, Philadelphia Mayor Michael Nutter said, with the water sending "couches, furniture, all kinds of stuff floating down the street." Two buildings collapsed in Philadelphia, Nutter told reporters, but no one was injured.
One family paid tribute to the storm by naming their child Manuel Hurricane Cooper, said Riddle Hospital spokeswoman Bridget Therriault in Media, Pennsylvania, just outside Philadelphia. Manuel was born at 12:01 a.m. Sunday,
Those living around the Gilboa Dam in upstate New York, about 50 miles southwest of Albany, were told to evacuate Sunday afternoon due to concerns that the dam could be overwhelmed by "higher-than-predicted amounts of rain."
Farther south in New York City, officials worked Sunday night to return the city to normal. Hours earlier, the Hudson River overflowed in lower Manhattan, receding only after massive amounts of water spilled over jogging paths and into at least one nearby apartment building. Water also lapped over the banks of the city's East River and onto Orchard Beach and Yankee Stadium parking lots in the Bronx.
There were no reports of deaths, though firefighters did help evacuate dozens from flooded homes in areas of Staten Island due to neck-deep water, the New York City Fire Department said.
Lines on the Metro-North system flooded, eroding tracks and causing significant damage, said Metropolitan Transit Authority chief Jay Walder. But as inspections and clean-up continued, the system -- which was shut down at noon Saturday -- took its first steps to returning with resumption of some bus services at 4:30 p.m. Sunday and planned restoration of some subway services at 6 a.m. Monday.
In addition, the Federal Aviation Administration announced that the area's three major airports -- Newark Liberty in northern New Jersey and LaGuardia and John F. Kennedy in the New York City boroughs of Queens -- will reopen Monday, two days after they shut down. NJ Transit rail service is suspended "until further notice," except for the Atlantic City rail line, but light rail and bus service will resume Monday.
"All in all, we are in pretty good shape because of the exhaustive steps, I think, we took to prepare for whatever comes our way," New York Mayor Michael Bloomberg said.
It's all due to a storm that first made landfall at 7:30 a.m. Saturday in North Carolina, then paralleled the coast, and slammed into Little Egg Inlet, New Jersey, as a Category 1 hurricane around 5:30 a.m. Sunday, the National Hurricane Center said.
Officials have reported six deaths in North Carolina, four in Virginia, four in Pennsylvania, two in New York and one each in Connecticut, Maryland, Florida, New Jersey.
In addition, one woman is "feared dead" in Vermont after being swept away in raging waters in Wilmington, Bosma said. Connecticut emergency management spokesman Scott Devico said one man has been reported missing in river-waters in the inland town of Bristol, while two individuals are unaccounted for in East Haven because authorities do not know their whereabouts after their home got swept away by the sea.
And the governor of Virginia, parts of which saw 16 inches of rain and top winds clocked at 83 mph, warned Sunday that more bad news may be coming.
"Undoubtedly, there will be more reports of damage, of injuries, perhaps fatalities," Gov. Bob McDonnell told reporters.
Flanking Obama during his afternoon statement, FEMA director Craig Fugate vowed Sunday that authorities will work with those impacted by the wind, rain, storm surge and resulting flooding.
"When the disaster comes off the news and no one is paying attention, we still don't go home," he said. "We know we've got a lot of work ahead of us."
CNN's Gary Tuchman, Poppy Harlow, Phil Gast, Greg Botelho, Divina Mims, Tom Cohen, Rob Marciano, Ali Velshi, Soledad O'Brien, Rose Arce, Jeanne Meserve, Chris Boyette, David Mattingly, Susan Candiotti, Chris Lawrence, Jason Carroll, John Zarrella, Kimberly Segal, Sarah Hoye, Holly Yan, Kristina Sgueglia, Eden Pontz, Gregory Clary, Elizabeth Cherneff, Samantha Stamler and Marina Landis contributed to this report.