The Long Island Rail Road will face off in court Wednesday with the Town of Brookhaven to decide the best way to address a 7.5-acre illegal LIRR dumping site in Yaphank.

The town is suing the LIRR and the State Department of Environment Protection over a railroad plan to pave over the 24-foot-thick dump site, about 1,000 feet from the Carmans River Estuary, where the LIRR admits to having discarded waste for decades beginning in the 1950s. All sides are scheduled to deliver oral arguments Wednesday in Central Islip before state Supreme Court Justice H. Patrick Leis.

In 2002, the DEC, under its now-defunct Voluntary Cleanup Program, agreed to the LIRR’s proposal to remedy the dumping site through a “cap and store” project. Under the plan, the railroad would contain the 100,000 cubic yards of contaminated materials by installing stone, concrete and asphalt caps.

But the town says, despite the DEC’s approval, the LIRR has a responsibility under state environmental law to remove the contaminated materials, which include lead, asbestos, mercury and arsenic that could seep into the groundwater.

“Really, the town’s point is if this dumper was anybody other than a state agency, the DEC would never have approved this plan,” said Garden City attorney Robert Calica, who represents Brookhaven in the suit.

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LIRR and DEC officials both said they could not comment on pending litigation. Brookhaven spokesman Jack Krieger also declined to comment Tuesday, other than to say that the parties in the suit “are in settlement discussions right now.”

The LIRR, in court papers, has said that the DEC has already determined that the site “would not pose a significant threat to public health or the environment,” and has chosen against including it on list of brownfields hazardous waste sites. But even if it were on the list, the railroad said the DEC “routinely considers both technical feasibility and cost effectiveness” in choosing a remedy, and the LIRR’s plan takes steps “to address reasonably foreseeable” health and environmental dangers

But the town, in its court papers, calls the cap and store plan “an insufficient cleanup alternative, which utterly fails to remove the hazardous materials from the LIRR dump site.” It says the state Superfund laws require the LIRR to “restore the site to pre-disposal conditions to the extent feasible.”

Richard Amper, executive director of the Long Island Pine Barrens Society, said, once all the facts are presented, he believes Leis will agree that the LIRR needs to clean up the site, which is in a groundwater protection area.

“These are areas where the greatest protection against contamination should occur, not the least,” said Amper, who believes the cost of a thorough cleanup should not be a factor. “It’s a little late now to be complaining that what was done is too expensive to remediate.”