The Environmental Protection Agency designated the Gowanus Canal in Brooklyn a Superfund site on Tuesday and announced plans to clean up more than a century’s worth of noxious pollutants there.

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.