Compared to cleaning the Gowanus Canal, tackling the larger, more heavily polluted Newtown Creek poses a far greater challenge. Also, a costlier one.

The U.S. Environmental Protection Agency (EPA) has proposed placing the polluted waterways on the National Priorities List, making them eligible for a Superfund cleanup, and is expected to list both sites.

The agency has estimated cleaning the Gowanus Canal would cost as much as $400 million. At a recent meeting, EPA official Walter Mugdan said it would “probably cost more” to take on Newtown Creek.

That would push the combined cost of cleaning both upwards of $1 billion, if not more, making the environmental remediation work among the most expensive projects in Brooklyn. To pay for the cleanup, the EPA plans to tap property owners along the canal responsible for its pollution.

Mugdan said the EPA is up to the task, though he cautioned considerable prep work remains to be done before the actual cleanup begins, if Newtown Creek is indeed listed.

He said it could take as long as 15 years to finish a remedial investigation/feasibility study, propose a suitable remedy, approve a record of decision and finalize a remedial design. Then the cleanup would start. (By contrast, the EPA expects the Gowanus Canal planning process to take 10-11 years).

“This site is a lot more complicated than the Gowanus Canal,” Mugdan said at the November 5 meeting, organized by the Newtown Creek Alliance and held at St. Cecilia’s Church in Greenpoint.

Newtown Creek is more than twice as long as the canal, and much wider. In addition, it remains an active industrial waterway, making the logistics of a comprehensive cleanup tricky.

Simply testing Newtown Creek in order to propose the site for Superfund status was a major endeavor, taking the EPA approximately three months to finish.

Completed this past April, the study showed the creek bed is contaminated with metals such as copper and zinc and various semi-volatile organic compounds, including high levels of PCBs. Newtown Creek was also the site of one of the world’s largest underground oil spills.

A Superfund cleanup won’t clean up the oil spill, however. That process is being negotiated using consent orders by the gas company Exxon Mobil and the state Department of Environmental Conservation.

Mugdan said the EPA would focus exclusively on cleaning the creek’s contaminated sediment - estimated at over 1 million cubic yards - not improving the water quality.

“That and only that is the focus of the proposed Superfund listing,” Mugdan said. He added later, “We’re not interested in the big Exxon Mobil oil spill. That’s not our lookout.”

Mugdan did say the EPA would examine upland properties along the creek to ensure future contamination is stopped before proceeding with a cleanup.

So far, with the public comment period winding down, the prospect of a federal government-led cleanup of Newtown Creek has generated far less controversy than the proposed Gowanus Canal project, which drew strong opposition from the city.

Nevertheless, some trepidation exists on the part of business owners with creek-side properties. If the waterway is designated, they argue, investment could be driven from the area. Besides, small businesses could be forced to pay for the cleanup.

“I’m really concerned about the potential for long-term destabilization of business in the area,” said Leah Archibald, executive director of the East Williamsburg Valley Development Corporation, a member-based organization of area business interests. “I’m worried it’s going to have an economic impact on the community.”

Mugdan said over time a clean waterway would improve the community and attract investment to the area.

Councilman-elect Stephen Levin, who will represent North Brooklyn starting in January, said he could throw his support behind a Superfund listing if upon further review an EPA cleanup emerges as the best solution.

“As someone who lives a block from Newtown Creek, and who cares about the community very much,” Levin said, “I want to see it cleaned up. If this is the most effective way, I would lean towards supporting it.”

Cleaning the Newtown Creek would be a long and complicated affairs, say EPA officials preparing to start the project.