The decision ended a contentious debate and was a blow to the Bloomberg administration, which had proposed a cleanup without such a designation. The city had argued that the label could set off legal battles with polluters, prolong the dredging operation and spook developers leery of the stigma of a Superfund listing.
But in a conference call with reporters, Judith A. Enck, the E.P.A. administrator for the region, said the Superfund designation would guarantee the best result for residents and the environment and ensure that the polluters cover all the costs.
“We believe that it would get us the most efficient and comprehensive cleanup,” Ms. Enck said.
From Gowanus Bay to New York Harbor, the agency has found contamination along the entire length of the clouded 1.8-mile canal in a preliminary assessment, including pesticides, metals and the cancer-causing chemicals known as PCBs.
The agency estimates that the project will last 10 to 12 years and cost $300 million to $500 million. The city estimated that its approach would take nine years.
The E.P.A., which proposed the Superfund designation last April at the urging of the New York State Department of Environmental Conservation, made its decision after a public comment period that involved more than 50 meetings with city officials, developers, community groups and others. Nine other Superfund sites across the country were also designated on Tuesday.
“It was the right thing to do,” said Marlene Donnelly, a leader of the neighborhood group Friends and Residents of Greater Gowanus. “It’s the beginning of a plan to start the restorative process for the Gowanus area.”
City officials expressed disappointment but struck a conciliatory tone and pledged to cooperate with the cleanup.
“But we are going to work closely with the E.P.A. because we share the same goal: a clean canal,” he added.
Carved out of tidal wetlands and streams in the 1860s, the Gowanus evolved into a busy waterway for oil refineries, chemical plants, tanneries, manufactured gas plants and other heavy industry along its banks. Industrial waste and raw sewage gushed into the canal for over a century.
Most of that flow has halted since the 1960s as maritime shipping faded. Today the 100-foot-wide canal is used for commercial and recreational purposes by neighborhoods bordering it, including Park Slope, Cobble Hill, Carroll Gardens and Red Hook.
Yet even as kayakers glide alongside the banks and fishermen catch striped bass for sport at its mouth at Gowanus Bay — the fish are too contaminated to eat — residents complain about the odors from continuing discharges of sewage and unsightly debris from scrap metal yards and other industrial enterprises.
The E.P.A. has already identified the city, the Navy and seven companies, including Consolidated Edison and National Grid, as potentially responsible for the past discharges. It is seeking additional information from at least 20 other companies so it can map out the financing of the cleanup.
“This is a historical puzzle we’re putting together here,” Ms. Enck said.
Caswell F. Holloway IV, a former mayoral aide who helped design an alternative cleanup plan for the Gowanus and is now the commissioner of the city’s Department of Environmental Protection, said he had no estimate of New York’s financial liability for what federal officials said included contamination from various facilities, including an asphalt plant and an incinerator in the area. He said the city would work with the E.P.A. to ensure that costs are recovered from all responsible parties.
“The city has an obligation to ensure that the burden is shared fairly,” Mr. Holloway said.
He noted that the administration had already committed $150 million to reducing odors and preventing sewer discharges and had shared the cost of a feasibility study for an environmental restoration project by the Army Corps of Engineers. E.P.A. officials said they saw those projects as complementary and expected them to continue.
Mr. Holloway said it was uncertain how the Superfund designation would affect economic development in the area.
One developer, Toll Brothers, said it would scrap its plan for a $250 million project with about 450 housing units and retailing space on three acres by the canal. “We wouldn’t be able to obtain financing to build, and we’d have difficulties obtaining insurance,” said David Von Spreckelsen, a senior vice president with the company, citing factors like uncertainty on how long the cleanup would take.
But Gowanus Green, a $300 million project for 774 units of new housing in nine buildings as well as retailing and community facilities, mostly financed by the city, is going forward.
“We’re in full support of the project, and we’ll work with the E.P.A.,” said Aaron Koffman, a spokesman for the Hudson Companies, one of the companies in the project’s consortium.
Eager to preserve such development potential, the city had proposed an approach under which the federal agency would allow the polluters to pay for the cleanup voluntarily.
But Ms. Enck said the city’s plan lacked “financial certainty” because it relied partly on federal allocations that would require Congressional approval. Agency officials also worried that having the Corps of Engineers and the E.P.A. both tackle the cleanup would complicate an already messy challenge.
In advocating for a Superfund listing, Ms. Enck had rejected arguments that it would keep investors and lenders away.
“Banks look at the environmental conditions of the properties,” she said at a meeting with reporters last week. “It is not a secret in Brooklyn that the Gowanus is contaminated. The notion that Superfund is going to create a stigma just doesn’t hold up.”
Agency officials said the cleanup, which will focus chiefly on the sediment in the canal, had effectively begun, with sampling already under way.
The timetable calls for completing the sampling and assessments of human and environmental risks by the end of the year. A full cleanup plan is to be drafted by 2014, with the work then unfolding over at least five years.
Walter Mugdan, the agency’s regional Superfund director, said that most of the canal would probably be dredged.
Additional steps include eliminating all sources of continuing contamination, like overflowing sewage and the migration of contaminants from groundwater under old industrial plants.