The decline of the Peconic Bay system as a healthy ecosystem is inevitable unless the definition of “business as usual” is changed by the state, the county and the operators of waste treatment systems.

Currently 79 sewage treatment plants and 796 large commercial septic systems that have permits to operate in Suffolk County discharge waste into surface or groundwater that fails to meet drinking water standards, according to Peconic Baykeeper Kevin McAllister. Eventually, the nitrogen these systems put into ground or surface waters make it into the bay system, where they encourage algae growth, which consumes oxygen and stresses fish and shellfish populations.

Mr. McAllister believes 70 percent of the nitrogen in the Peconic Bay system may come from treatment system wastewaters, as was proven to be the case in Great South Bay, according to the county’s Comprehensive Water Resources Management Plan. Some of it also comes from the thousands of small residential septic systems that dot the upland around the bay system; fertilizer residues that seep in runoff from lawns and farms; and some of it comes from animal waste, such as geese.

On the 40th anniversary of the federal Clean Water Act, Mr. McAllister announced recently that he had petitioned New York State to modify 1,338 State Pollution Elimination Discharge Permits under which all sewage treatment and commercial septic systems operate in Suffolk County.

He wants the state to impose tougher standards and require operators to use the newest technology to reduce nitrogen emissions. He’s supported by County Legislator Ed Romaine. “We’ve allowed the proliferation of inexpensive, inefficient sewage treatment systems,” Mr. Romaine said of county and state regulators.

How ironic it is that the Clean Water Act has been turned into a law that actually sanctions pollution when it comes to systems that are covered by State Pollution Elimination Discharge Permits. If things don’t change, the impairment of the bays will continue and we’ll all be the worse for it.