A barge carrying toxic waste dredged out of Brooklyn’s fetid Gowanus Canal has sunk — potentially delivering the muck right back into the water again, the Environmental Protection Agency revealed Tuesday.

The barge — part of the EPA’s “Superfund” effort to clean the notoriously filthy waterway — went down in nearby Gowanus Bay Monday, and remained submerged as of Tuesday afternoon as crews attempt to pump it dry “during periods of low tide,” the EPA said in a statement.

Federal regulators are “actively investigating the incident to determine the cause, whether contaminated sediment was released into the water and to determine appropriate next steps,” the agency said.

“Dredging activities have been temporarily suspended so that crews can concentrate on operations to secure the barge.”

The $506 million Gowanus Canal clean-up got underway last year — more than a decade after the EPA declared it a Superfund site marked for high priority.

The federal effort involves dredging and other work along the First Street turning basin and other sections of the 1.8-mile canal, which was one once dubbed “Lavender Lake” for its purplish chemical hue.

As part of the clean-up, small barges dredge up the waste material, which is transferred to a larger watercraft that ships it out to New Jersey, according to Brooklyn Paper.

The waterway was long a dumping ground for industrial waste and raw sewage.

In 2007, scientists discovered the canal was not only toxic, but also infected with gonorrhea.