“You’re looking at significant expenditures of money to make the plants more secure,” said John Cameron, an engineer who specializes in wastewater-treatment facilities and is the chairman of the Long Island Regional Planning Council. “There is no Band-Aid for this,” he added. “This is the new normal.”

When the plants are fully functioning, they treat incoming sewage to remove solid waste and toxic substances and kill bacteria before it is discharged into the ocean or a bay. When the plants are shut down, the raw sewage goes into waterways in the same condition as when it comes in. At least six sewage plants in the New York region shut down completely during the storm, and many more were crippled by storm surges that swamped motors and caused short circuits in electrical equipment.

In New Jersey, workers at the Passaic Valley Sewerage Commission plant, the fifth largest in the country, had to evacuate as floodwaters surged in and wastewater gushed out.

The Middlesex County Utility Authority plant in Sayreville, N.J., let about 75 million gallons of raw sewage a day flow into Raritan Bay for nearly a week before power was restored, said Larry Ragonese, a spokesman for the State Environmental Protection Department.

Operations at both plants have not yet been fully restored.

The damage to the plants did not cause contamination to drinking water, which is run through separate systems, officials said. In some areas, officials imposed restrictions on water use to reduce strains on plants.