The smell of sewage isn’t the only thing hanging over the Gowanus Canal as the Environmental Protection Agency begins public review of its proposed cleanup plan for the Superfund site.

One critical question lingering in the air is what exactly the City of New York will have to pay for its role in the cleanup. Also unknown: what measures the city’s Department of Environmental Protection will take to curb the raw sewage that continues to pour into the murky waters.

Photo: brainware3000/Flickr

It’s been nearly three years since the Environmental Protection Agency won out against the Bloomberg Administration in their competing efforts to take charge of the notoriously polluted Brooklyn canal. It became a national Superfund site in March 2010, much to the chagrin of NYC officials.

But the city will nevertheless play a central role in the future of the urban water body, because as the source of the sewage it is likely to be identified in the Superfund review as one of the polluters responsible for paying to clean the canal back to health.

Last week, the EPA held public meetings in Carroll Gardens and Red Hook, two of the communities flanking the canal, to roll out its proposed plan for cleaning up the toxic waters. For decades, all manner of industry — gas and chemical plants, oil refineries, paint factories, cement makers and tanneries — surrounded the two-mile-long, manmade canal, releasing chemicals and metals that now sit in unsightly sediment that the EPA describes as “black mayonnaise.” Covering the native sediment, it lays in accumulations that average 10 feet thick. Constant sewage overflows continue to contaminate the waters.

The EPA’s testing of the sludge not only revealed troubling levels of metals like lead, arsenic and mercury, but also polychlorinated biphenyls (PCBs) — a group of chemicals banned several decades ago because of their health effects — and polycyclic aromatic hydrocarbons (PAHs), chemicals that vaporize easily and have been linked to cancers and mutations. The PAHs have traveled all the way down into the canal’s natural sediment — the earth that was there before it was made into a canal — along with oil and solvents.

The EPA’s task under the Superfund program is to clean up the sediment to the point that it is no longer poses a risk to humans and animals, and to prevent future contamination. Its plan is to dredge all the toxic sediment in the canal and then create layers of sand and gravel to prevent contaminants from migrating up from the polluted bottom layer of native sediment into the waters above.

Based on the level of contamination, which varies throughout the canal, the agency would treat the sediment to the point that could be reused elsewhere, or just dispose it on site. Depending on which option the public and the EPA ultimately settle on, the agency estimates treatment and disposal of the sediment will cost between $179 million and $216 million.

All told, the EPA estimates that the price tag for the Gowanus cleanup will total between $467 million to $504 million — and under the law, those costs must be borne by the polluters.

Part of the EPA’s work when it takes on a Superfund project is to identify the parties responsible for the pollution so that those entities, rather than taxpayers, will pay for the cost of clean up. In this case, however, the city of New York is likely to be one of the responsible parties.

EPA spokespeople note that it is not unusual for a local government to be liable for costs or to be involved in Superfund clean up efforts in some way. If the city ends of paying, the expenses would likely show up as a capital budget item, paid for in taxpayer funds, according to Doug Turetsky, chief of staff for New York City’s Independent Budget Office.

EPA spokesperson Elias Rodriguez said it’s too early to say how much the city could end up paying. The agency is still in the process of collecting information from potentially responsible parties. The details of who will have to pay, and how much, won’t come until after the EPA finalizes its plan, Rodriguez said. As of January, the agency had identified 31 potentially liable entities, and has requested documents from them and more than 73 other companies to help determine those costs. Theoretically, those that polluted the most will pay the most.

The agency is scheduled to select its remedy this summer, after collecting public comments through March, and complete a design in 2016. It projects that the remediation will wrap up in 2022.

But the city can’t just write a check and wash its hands of the Gowanus pollution. The EPA has already called on the city to take actions that would prevent further contamination in the canal. The water body is routinely inundated with raw sewage from the city’s combined sewer and storm water systems, outdated infrastructure that becomes overwhelmed in times of heavy rain and overflows before the waste is carried to a treatment center. Following superstorm Sandy, levels of sewage-borne enterococcus bacteria reached more than 230 times the EPA’s acceptable levels.

The city is already working to reduce overflows by one-third at points in the middle and lower reaches of the canal, in a project overseen by the state Department of Environmental Conservation. But the EPA has also called on the city to construct two storage tanks — one that would hold four million gallons, one eight million gallons — that would capture any overflow sewage before it got to the water. It estimates that the cost would be $78 million.

At the public meeting in Carroll Gardens last week, residents aired doubts that the city would commit to the tank project, especially following remarks by Angela Licata, deputy commissioner for the New York City Department of Environmental Protection. Licata said the agency was still collecting data and considering its options, and noted that retention tanks for sewage are expensive to build and maintain.

The possibility that the city could subvert the EPA’s demands for action on the storage tanks has introduced uncomfortable uncertainty to the cleanup project. But Hans Hesselein, director of special projects for the nonprofit Gowanus Canal Conservancy, says he is nevertheless heartened by the EPA’s work in the area.

“Things continue to move forward at a rapid pace,” he said. “We are impressed.”

Also impressed, it would appear, were the succession of area residents at last week’s meeting who cheered on EPA employees when they were introduced and stood in line to offer their thanks and ask questions.

Judith Enck, the Region 2 administrator for the EPA, said at the meeting that though the canal’s flooding during Sandy didn’t spread contaminated sediment the way some had feared, it was a wake-up call regardless.

“It illustrated the need to get this urban waterway cleaned up as comprehensively and as quickly as we can,” she said.