Corrosive saltwater chemicals -- left after superstorm Sandy three years ago flooded a pair of East River tunnels used by the LIRR -- are eating away at concrete walls and tracks, and repairs are still years away.

Engineers contend the century-old tunnels owned by Amtrak are structurally sound and pose no imminent safety threat, but their crumbling walls can and have caused major problems for trains, including chronic delays.

Damage to the tunnels from the October 2012 storm is significant: cracks, some as wide as half an inch, stretching across hundreds of feet inside; holes in concrete walls and the tunnels' linings as large as 3 square feet and so deep that they have exposed steel rebar hidden beneath; and cast-iron bolts in the tunnels' linings stressed nearly to their breaking points under the "unprecedented" load of Sandy's floodwaters, according to a September 2014 report.

"The tunnel is safe," Amtrak said in a statement Friday, noting that the structures' cast-iron ring and linings are intact and that workers routinely conduct inspections. "Each tube is physically walked and inspected twice a week by track inspectors who report any obvious change of condition. Any loose concrete is removed and spot repairs are made as necessary on any noted anomalies."

Amtrak is putting together a plan to repair the damage, but has said it doesn't have the money for the work, in part because a federal court ruling limited the insurance payout to Amtrak for the tunnel damage to just $125 million. The report estimated the work will cost more than $330 million. Amtrak is hopeful that an appeal will overturn the court ruling and also believes it could find funding through federal sources.

Even with the money in place, Amtrak has said commencement of the repair work is still four to five years away.

advertisement | advertise on newsday

"They need to get with it," said Sen. Chuck Schumer (D-N.Y.), who has said he is working to find federal funding for the project but wants it to be a high priority for Amtrak, which has lobbied extensively to replace its Hudson River rail tunnels that sustained significantly less Sandy damage. "Amtrak needs to give the East River Tunnels far more attention."

The biggest culprits behind the damage in the tunnels are chlorides and sulfates from the saltwater that entered the tunnels from Long Island City and filled the passageways, from floor to ceiling, for thousands of feet.

Ongoing damage, delays

Of the four East River tunnels, the two tubes that were flooded -- known as lines 1 and 2 -- are used the least by the LIRR. Still, about 30 percent of all trains running through the affected tunnels are operated by the LIRR, the railroad said.

"Following Sandy, the tunnels have been and are being damaged by the effects of the salts left behind," according to the report, prepared by Kansas City, Missouri-based HNTB Corp. "The chlorides began to attack the rail system in the tunnels . . . and this damage is continuing."

The salts do their work in several ways, including by making concrete more porous, drawing in moisture and corroding steel.

Nowhere is the saltwater damage inside the tunnels more apparent than along the structures' concrete bench walls that run parallel to each other along either side of the tracks and house wiring and other equipment.

According to the report, "severe cracks," including one stretching 500 feet, are common throughout the walls, as were "very deep" holes -- some more than a foot in depth -- caused by chunks of concrete breaking off.

The report noted that when those pieces fall onto the tracks, emergency repairs and train delays could occur.

"Unless the damaged bench walls are replaced, such incidences will continue to worsen due to the process known generally as chloride attack and sulfate attack," the report said.

advertisement | advertise on newsday

The LIRR has already reported that the number of train delays caused by Amtrak has nearly doubled since 2012.

Despite the damage, the report found no indications that the support structures for the underwater passageways were "unsound," meaning that there is no imminent risk of collapse.

Fletcher Griffis, a civil engineering professor at New York University's Tandon School of Engineering, said that, if neglected, the ongoing damage to the concrete in the tunnels could eventually compromise their structural integrity, but that is likely several years away.

But falling chunks of concrete do pose safety threats, including by causing derailments, as happened to a Brooklyn subway train last month.

"It's not something that you think about as a near-term, catastrophic problem. But it needs to be fixed," said Griffis, who also serves as director of the New York State Resiliency Institute for Storms and Emergencies. "I'd say it's something you've got to watch very closely, but I'm sure these guys are doing that."

advertisement | advertise on newsday

Yearlong closures

Amtrak has said the repairs will require shutting down each of the two affected tunnels for one year.

Although those tunnels are used more by Amtrak and New Jersey Transit -- which stores trains in Queens -- the outages will be felt strongly by the LIRR because Penn Station will have far less total capacity.

LIRR president Patrick Nowakowski said he would prefer that major repairs be deferred until after the railroad gains a second Manhattan station as part of East Side Access to link the railroad to Grand Central Terminal.

Until then, he said he believes all of the railroads using the tunnels should continue to closely inspect them.

But, Nowakowski said, doing nothing is not an option.

"You need to fix the asset. You don't need to run it into the ground and have it fail catastrophically, or just deteriorate to the point that this ain't going to work," Nowakowski said in June. "That's the wrong approach. I'm an engineer. I believe in fixing it."

Nowakowski said his priority is to work with Amtrak on getting the two unaffected tunnels in as good a shape as possible before either of the other tubes are taken out of service for repairs.

Other post-Sandy work

Elsewhere, the LIRR's post-Sandy repair work is well underway, officials said. The LIRR identified $300 million in necessary fixes and has begun $200 million in work.

On the Long Beach branch, which was hit hardest by the storm, the LIRR this year completed installation of one of three new electrical substations, and began construction on a second. A new emergency electrical generator for the Wreck Lead Bridge is also now in place.

The Federal Transit Administration has also approved $100 million in resiliency projects for the LIRR, including hardening the Queens portals for the East River Tunnels against flood surges.

"There is still a lot of Sandy work to be done, so we are not hardened to the point that we'd like to be," Nowakowski said. "But that work is ongoing. And every day, it progresses a little bit further."