What would the FEMA flood zones released this week look like flooded with water? Now you can see.

As the city of Boston has picks up the pieces from last weeks’ bombings, and Texas struggles with droughts and the aftermath of explosions, the Midwest has been facing some of the worst flooding they’ve ever seen.

Up and down the New Jersey coast, municipalities from Sea Bright to Ortley Beach are reporting increased incidences of flooding, even in places that don’t normally flood. But officials don’t agree on why it’s happening or how to stop it.

One World Trade Center with 9/11 in the foreground. (photo by melfoody / Flickr)

(New York, NY - WNYC) A Port Authority of New York and New Jersey official says a built-out World Trade Center site will be less vulnerable to future storms like Sandy once construction is done by 2020. But the authority hasn't decided what to do in the meantime to protect the site from rising tides.

Construction sites that include open pits, as does the 16-acre World Trade Center site, are vulnerable to flooding. And much of the site is built on landfill where the Hudson River once flowed--and would flow again if not for retaining walls.

But Port Authority executive director Pat Foye wouldn't elaborate on what steps could be taken to protect the site from flooding while under construction, and harden the site once construction is done in an age of climate change and rising sea levels.

"Port Authority people and outside experts are looking at how to make the site more resilient," Foye said. He wouldn't give details about possible mitigation efforts beyond saying, "The review continues."

Foye estimated it will cost $2 billion to repair storm damage to the World Trade Center, along with the rest of the authority's facilities, including airports, bridges and tunnels. Foye said $800 million alone is needed to fix the PATH train system, which only recently returned some of its lines to a pre-Sandy schedule.

Foye said insurance reimbursements and FEMA payments should cover those costs."There will be no material impact on the budget," he said.

Still under construction in Lower Manhattan is One World Trade Center, which carries a price tag of $3.8 billion, making it the world's most expensive new office tower. To offset the costs of the 1,776-foot skyscraper, the authority last year levied higher bridge and tunnel tolls and reduced spending on transportation infrastructure.

One World Trade Center is scheduled to be done by early next year. But some part of the larger World Trade Center site will be under construction, and vulnerable to flooding, for at least the next eight years.

High wind and heavy rain caused delays at local airports, thousands of power outages throughout our region, and flooding in places along the shore in New Jersey Friday.

The New York City Council announced a package of legislation on Tuesday that seeks to improve the city’s infrastructure in the aftermath of Sandy, as well as better prepare the city for future storms.

(Nancy Solomon, New Jersey Public Radio) A year before storm Sandy, federal officials warned transit agencies to get their trains out of flood zones in advance of severe storms.  But New Jersey Transit, the nation's third largest transit agency, didn't heed that advice.

Maps produced in 2009 by the Army Corps of Engineers, taking into account storm dynamics and shoreline elevation, showed NJ Transit's rail yards well within potential flood zones for a Category 1 or larger hurricane.

Even as New York's MTA was moving subway and commuter trains to higher ground, NJ Transit parked valuable trains squarely in the middle of known potential flood zones for a Category 1 hurricane -- the equivalent of New York City's evacuation "Zone A." While the MTA had much of its system up and running within a week,  NJ Transit has taken much longer.

A spokesman for Governor Chris Christie says the trains were stored in in places that had never been inundated before. "You can prepare for a worst-case scenario," the spokesman, Michael Drewniak, said.  But, he added "the standard of preparedness was definitely raised by this storm."

In an interview with the NJ Star-Ledger published Wednesday, NJ Transit officials maintained the trains were stored where they "should be."

A year earlier, however, the Federal Transit Agency had distributed a report on climate change adaptation called "Flooded Bus Barns and Buckled Rails."  The study warned transit agencies to prepare for worsening storms and floods. New Jersey Transit has not released a detailed accounting,  but Reuters has reported damage to trains could cost tens of millions of dollars.

One tube of the Brooklyn Battery Tunnel (now known as the Hugh L. Carey Tunnel) is now open to traffic, and New York's MTA has released a video of the recovery process.

Hurricane Sandy flooded the tunnel with millions of gallons of sea water "from floor to ceiling," according to New York Governor Cuomo. (Exactly how much water isn't clear. Earlier reports said the tunnel had taken on 43 million gallons; in the above video, the tunnel's manager, Marc Mende, says the tunnel was flooded with 80 million gallons. Whatever the amount, you can see footage of water in the tunnel at about 38 seconds in -- and it's daunting.)

That was a new experience for the MTA's tunnel employees. "We've never had a leak," said Mende. "We never had a puddle. The only water we ever had in this tunnel came off of vehicles."

The Brooklyn Battery Tunnel remained completely closed to traffic for over two weeks while workers pumped out the water and repaired electrical, lighting, communications, surveillance, and ventilation systems. Cuomo says it will another "few weeks" before the second tube is open.

Here's the scene, after Sandy:

New York University Langone Medical Center reopened many of its outpatient offices, and the 600 students in the medical school went back to classes – but it’s still not clear when the hospital will open its emergency room, surgical suites and labor and delivery ward.

Staten Island was one of the areas hit hard by massive flooding from Sandy. Among the people that stayed, was the family of 17-year-old Tasina Berkey, a current Radio Rookie. Her family, like many of their neighbors, never experienced flooding like this before.

The totality of the damage done to New Jersey Transit by Hurricane Sandy can't be fully ascertained at this point, but the list on the agency's website is daunting.

Rail lines have suffered catastrophically: washouts, downed trees, waterlogged equipment, and track damage. The iconic Hoboken Ferry Terminal is flooded. The agency reports that even the Rail Operations Center--"the central nervous system of the railroad"--is engulfed in water. Although most bus service returned Thursday, nine of its bus garages continue to operate on back-up generator power. And in a letter requesting federal aid, Senators Lautenberg and Menendez write: "the only passenger rail tunnel into New York City—which connects thousands of people to the city each day—is shut down."

Earlier this week, Governor Christie said it could take seven to 10 days to resume PATH train service.

There is no timeline for resumption of rail service. The agency says it is continuing to inspect the system and that "the blow delivered by Hurricane Sandy will continue to impact customers for days to come."

New York's MTA just released a startling video of the extent of the flooding at the South Ferry - Whitehall station, located at the southern tip of Manhattan.

The station recently underwent a $530 million overhaul. When it reopened in 2009, it created a new connection between the 1 train to and N/R line and was the first new subway station in the city to open in 20 years.

Below, for comparison, a photo of the station pre-Hurricane Sandy.

We’ll be updating this throughout the day. Send your photos to transponation@gmail.com or @transportnation.  ‘Cause we’d like to share them.

1:3opm: broken traffic light at King Street and Varick Street in lower Manhattan (photo by Kate Hinds)

10:27: from Jim O'Grady: "World Trade Center. Cop said PATH station flooded, didn't know how badly. My guess: badly."

10:11am: A beheaded subway entrance. (photo by Jim O'Grady)

10:11am: Staten Island Railway's Clifton Shop in the aftermath of Hurricane Sandy. (Photo by MTA via flickr)

9:55am: flooding at the entrance to the Hugh L. Carey (formerly Brooklyn Battery) Tunnel, via @NYGovCuomo

9:49am: Downed tree in Tribeca park (photo by Jim O'Grady)

8:14am: Rainbows over Brooklyn (photo by Andrea Bernstein)

The entrance to the downtown 1 train at Broadway and 79th Street (photo by Kate Hinds)

(With reporting from Alex Goldmark and Andrea Bernstein) Earlier Monday, the head of New York's Metropolitan Transportation Authority said that salt water from the East River would put the city's subway system “in jeopardy.”

So when word went out earlier Monday night -- from the agency's official Twitter feed -- that the doomsday scenario of salt water flooding the system could be coming to pass, New Yorkers feared the worst.

The tweet: "Up to four feet of seawater is entering subway tunnels under the East River."

But now the authority says that was an error -- and it can't ascertain the condition of the tunnels right now. From a tweet just before 9:30pm: "Correction: Condition of under river tunnels unknown. Up to four feet of water was observed at a Lower Manhattan station."

Salt water could corrode the subway's signal system. And even after water is pumped out of a flooded station, salt deposits remain behind. The MTA says these damaged signal systems can't always be cleaned in the field and sometimes they must be replaced outright.

The subway system was shut down Sunday at 7pm. The mayor said earlier Monday that it would not be up and running by Tuesday morning, which gives the authority more time to determine the condition of the system.

The MTA says the pumps for clearing water from the stations are running on generators, not dependent on Con Ed -- one piece of luck for the agency, given the power outages in the area.

A spring nor'easter along the East Coast on Sunday is expected to bring rain and heavy winds and even snow in some places as it strengthens into early Monday, a punctuation to a relatively dry stretch of weather for the Northeast.

New York Governor Andrew Cuomo is asking New Yorkers to help out upstate communities devastated by flooding earlier this year by donating items to a holiday drive.

Property owners in 13 New Jersey towns may be able to sell their homes to their local government, if they have suffered repeated flooding, through program that relies on funding from FEMA, the Federal Emergency Management Agency.

With Sea Level Rise, Subways Flood in 40 Minutes During Intense Storms (Map Courtesy LDEO & Civil Engineering, Columbia University)

On the Sunday after Tropical Storm Irene blasted through the five boroughs of New York City, the city exhaled. Huge swaths of Manhattan hadn’t flooded, high winds hadn’t caused widespread damage. Perhaps no one was as relieved as then-MTA CEO Jay Walder, who had just taken the unprecedented step of shutting down the entire transit system.

“The worst fear that we had, which was that the under-river tunnels on the East River would flood with salt water, were not realized. We certainly dodged something there,” Walder said at a post-Irene briefing with city officials.

Listen to the audio:

If this sounds like dystopian fantasy, consider this: the Federal Transit Administration is now advising transit agencies to start adapting to climate change. “Climate change impacts are occurring now and will increase in the future,” reads the first line of an FTA report, Flooded Lines and Buckled Rails: Public Transportation and Climate Change Adaptation, released in August. “Aggressive action to reduce greenhouse gas emissions will lower the severity of climate change impacts. Yet the amount of long-lived emissions already in the atmosphere means that a significant level of climate change is inevitable.”

“We have seen significant extreme weather conditions,” says Deputy FTA Administrator Therese MacMillan in an interview in the U.S. Department of Transportation’s Washington, DC headquarters. “The patterns are pretty indisputable. The hundred-year floods are occurring every 20 to ten years. The hurricane intensities are repeating themselves and being very common. The extreme winter effects that we’re seeing in the Northeast are clearly in evidence. We need to deal with the fact that these extreme weather conditions are impacting our already stressed transit infrastructure.”

She continues: "To not address it would be a relatively naïve response to the fact that there are millions of dollars on the ground that, as responsible stewards of the taxpayers money, we need to do the best job we can to deal with them. Whatever arguments folks want to have about the sources of the impacts, we’re seeing impacts.”

And with Irene, according to Columbia University professor Klaus Jacob, one of the nation’s foremost experts on transit and climate change, the city came perilously close to seeing just the kind of flooding that the FTA wants transit systems to protect against.

The price tag for that protection, Jacob says, could be as much as $15 billion -- at a time when the MTA is already $10 billion short in funding its current capital plan.

Klaus Jacob With His Model of Subway Flooding (Photo: Andrea Bernstein)

As it happens, one part of the system saw exactly what the FTA report warned of during Irene. About 35 miles  north of the city, on the Port Jervis line, the MTA saw what the line manager, Fred Chidester, describes this way: “In over 28 and a half years I have not ever seen anything to this magnitude on any of our lines.  And the type of damage that was done is just unthinkable.”

Fourteen miles of the Port Jervis line were washed away during Irene. The Ramapo River, which is usually little more than a creek in some areas, was already swollen by a month of unusually heavy rains even before Irene hit, causing it to transform itself like some water-infused Incredible Hulk.

Chidester took me on a tour of the line, where workers are now furiously trying to get the tracks up and running by the end of the month. He showed me where the river had carried boulders, larger in diameter than a full-grown man, from under the tracks to a location 50 feet away. “Both tracks were hanging in the air,” Chidester recounts, “and the whole area underneath them for about 15 feet in depth was totally washed out.”

An MTA video taken just days after the flooding show tracks twisted as easily as pieces of chewing gum, mangled into undulating waves. “That water could do this,” Chidester tells me, his voice trailing off into silence as he shakes his head.

The tracks of the Port Jervis line, following Tropical Storm Irene (image courtesy of NY MTA)

The Port Jervis line serves about 2,600 people a day. That’s tiny compared to the 5.2 million who ride the subway, but for those 2,600, the commute has been maddening. Those who ride the line are already super-commuters, with commutes easily two or even two-and-a-half hours. Even when it’s running properly, to get to or from Manhattan, riders have to switch in Secaucus or Hoboken. The line then travels through northern New Jersey to Port Jervis on the Delaware River, about 90 miles upstate, making a hook at the end.

After Irene, the line was cleaved in two.  Right where it crosses into New York and up to Harriman, the tracks have been unusable..The MTA provides buses, but the switch from the train to the bus causes both delays and anxiety. Jen Weisenberg’s commute now takes almost three hours. “I was hysterical crying. I was cursing my boyfriend out. I was asking why did I move here.”

Another view of the tracks of the Port Jervis line (image courtesy of NY MTA)

But the outage isn’t just inconvenient. The MTA invoked emergency powers to repair the Port Jervis line, at a cost of $50 million -- money it surely doesn’t have. A year and a half ago, to save money, the MTA cut some far-cheaper bus lines because its budget has been so stressed. But not fixing the line, for the MTA, is unthinkable.

Adding to the costs are a set of preparations to mitigate or prevent future flood damage. Chidester shows me where special culverts have been built under the tracks to absorb the force of the water. The ballasts are being shored up.

Metro North's Fred Chidester Shows New Drainage Pipes Under the Port Jervis Line (photo: Andrea Bernstein)

It’s hard to figure out how much extra that’s costing, because neither the MTA nor any railroad operator has experience this kind of washout in modern history. But, as Chidester says, “there’s no choice. I work for a railroad. I want to see trains running. I want to make sure they’re running right in the way they are advertised.”

Chidester says he’s no climate scientist. After trying to keep the line running through the worst snow season on record last year, and this October’s early storm, Chidester says he’s not sure about global warming. But the MTA is.

Projjal Dutta was hired by the MTA about five years ago to “green” its operations. But Dutta started just after a “freak” storm shut down the subway during rush hour in August, 2007, and his job morphed into something else: developing the MTA’s “climate adaptation” response. Making sure that the authority’s commuter rails can better withstand intense storms is part of that effort.

The MTA's Climate Adaptation Specialist, Projjal Dutta

But a lot of what Dutta does is focused on keeping water out of the subways. He takes me down to a subway vent in lower Manhattan. Most subway vents are flush with the sidewalk, like those “made most famous by Marilyn Monroe,” Dutta says.

When storm run-off rushes down city streets, it can run right down those storm drains into the subways. “With climate change and frequent flooding events and ever-higher water marks, their old levels were just not enough.” So the MTA has raised them about six inches, so floodwater will flow around them and into the storm drains -- not the subways.

Raising Subway Vents Prevent Subway Flooding During Storms (Photo: Andrea Bernstein)

There are other things the MTA is doing: platforms on the brand-new Second Avenue Subway and Number 7 lines will be “air tempered.” This century, stations will be hotter.

“We have to get that heat out,” Dutta says. “This is not for something as superficial as personal comfort, there’s lots of electronics that a train carries. We had a lot of heat related problems, so we’ve had to introduce cooling into areas that did not hitherto require heating.”

Dutta speaks matter-of-factly, but his words carry a punch. “Our core mission is to provide trains, buses, and subways.” Climate change adaptation, he says “takes something away from that core mission. If you did not need the air tempering, you could have built another station.”

He continues: “If there were more public transportation there would be less of this problem. It is ironic (that) in order to fight this greenhouse gas problem, resources have to be diverted from the regular running of a system. That’s a real tragedy.”

But perhaps not as tragic as having the entire system flooded, an eventuality that Columbia’s Klaus Jacob says is real. Jacob has worked with the MTA to model what would happen if you couple sea level rises – the FTA says to expect four feet by the end of this century – with intense storms like Irene. In forty minutes, Jacob says, all the East River Tunnels would be underwater. Jacob says he took those results to the MTA, and asked, if that happened, how long would it take to restore the flooded subway to a degree of functionality?

“And there was a big silence in the room because the system is so old. Many of the items that would be damaged by the intrusion of the saltwater into the system could not recover quickly.  You have to take them apart. You have to clean them from salt, dry them, reassemble them, test them and cross your fingers that they work."

In a best-case scenario, Jacob calculated that it would take 29 days to get the subway working again. But in the meantime, a halted subway would almost halt the city’s economy, which, he says produces $4 billion a day in economic activity.

The thing is, Jacob says, the city came within a foot of that happening during Irene. Because the astronomical tides were so high, and the storm so intense, the storm surge mimicked a future where the sea is much higher than it is now. During Irene, Jacob says, the storm surge was 3.6 feet. “Had it been not 3.6 feet but 4.6, we would have been in deep trouble.”

Manhattan Flood Zones Under 4-Foot Sea Level Rise (Map Courtesy LDEO & Civil Engineering, Columbia University)

Remember what Jay Walder said at that Sunday afternoon briefing?

“The worst fear that we had, which was that the under river tunnels on the East River would flood with salt water, were not realized. We certainly dodged something there,” Walder said.

This time.

As for the Port Jervis line, after $50 million in emergency repairs, repaired tracks are expected to be open by months’ end.

In Thailand, flooding has plagued large areas of the country since July, and now it appears to be headed for the city of Bangkok. Prime Minister Yingluck Shinawatra has issued an evacuation warning for suburbs of the area, which caused many citizens there to panic. Flood waters are flowing south toward Bangkok, and have already affected northern parts of the city.