PORTLAND, Maine (NEWS CENTER) — Major changes are taking place in downtown Portland that may have huge benefits for the health of Casco Bay.

The state Department of Environmental Protection (DEP) recently issued a five-year wastewater discharge permit, with the goal of reducing harmful pollution from the bay.

It involves an unlikely partnership between the Portland Water District and the Friends of Casco Bay.

Turns out nitrogen is in many things we throw out without thinking twice. Just beyond East End Beach, below Munjoy Hill, there is a spot called Pomeroy Rock where the majority of Portland's nitrogen enters the Casco Bay through a pipeline carrying treated wastewater.

"It's about 65,000 people, industries, commercial activity, so it's all pollution coming here," said Scott Firmin, director of wastewater treatment at Portland Water District. "We're treating it … by removing about 95 percent of what comes in."

Firmin's office literally overlooks the same harbor he's intent on protecting: Casco Bay. At the Portland Water District, he is responsible for dealing with the immense waste put out by the Greater Portland Area.

As we walk outside to the treatment tanks, he explains the process: "The solids settle to the bottom. We've got what we call clarified effluent at the top – that's what goes out to get disinfected."

It's a dirty job, carefully handled within the multi-level Portland Water District complex on Munjoy Hill. A popular walking path divides the facility's exterior wall from the ocean below.

"We're not polluters," Firmin said. "We're taking what would be pollution and we're treating it, removing it and then managing it in a safe way that it's not impacting the environment."

Chlorine added to the waste removes the majority of what's known as pathogenic bacteria as well as viruses.

"And then, right there, we're adding a chemical to remove chlorine," he said.

A $12 million upgrade to the wastewater plant's aeration system goes after something else: nitrogen.

"There's a whole slew of bacteria that can do that for you," Firmin said,  "and our goal is a 20 to 40 percent reduction from current levels."

That may not seem like much, but those watching the harbor closely call it an enormous first step — it means 500 to 1,000 fewer pounds of nitrogen going into the harbor every day.

As he stands at the controls, Peter Milholland prepares to pilot the Casco Baykeeper boat. He runs the Friends of Casco Bay Citizen Stewards Program, run by volunteers who monitor the bay's health.

"People come here because they know it's a beautiful region in the state of Maine," Milholland said. "All of our volunteers are collecting data all at the same time. It's called synoptic sampling — they collect once in the morning at 7 and then again at 3 in the afternoon — and so we can look at the health of the bay, across the bay at the same time at both morning and afternoon to see how the bay changes within a day."

And that data has revealed a disturbing trend of changes triggered by nitrogen: "There are places where people cannot recreate, where the algae are so thick it's like trying to go through jello," Milholland said.

Almost immediately after taking over as Casco Bay keeper, Ivy Frignoca identified algal blooms, fed by nitrogen, literally choking out life on the mud flats where shellfish live.

"And what we saw, for example in mill cove this past summer, was that the clams underneath all of it, they were very stressed out," she said. "They had their siphons sticking way out – which is a real sign of stress – and were trying to get to oxygen. Within a week, most of them were dead."

Her concerns are well-founded.

About 533 miles south of us, the Chesapeake Bay area is dealing with low-oxygen dead zones — places so choked by harmful algae blooms the water is clouded and discolored and cannot sustain fish or birds. And it's all traced to high levels of nitrogen.

"It's a complex problem because it involves algae," Frignoca said. "It involves dissolved oxygen – a lot of things that people just don't see."

A problem that residents surrounding Casco Bay have at least "some" control over — everything we flush, the showers we take, the runoff and storm drain pollution from our lawns treated with pesticides and animal waste not properly disposed of.

Firmin said part of his goal is to better educate Mainers to take responsibility for cutting back their own nitrogen waste.

"We're trying to figure out how far we can take things, while we understand what's happening out in Casco Bay," he said.

The Portland Water District and the Friends of Casco Bay working together for the health of a body of water that gives so much to all of us.

"We think it's going to make a world of difference, but we all have to continue working on it and figuring out the rest of the picture," said Frignoca.

She said these next five years will give all of them and the DEP the chance to conduct critical studies on the health of Casco Bay, keeping a very close eye on nitrogen levels with the ultimate hope of keeping the dead zones at bay and keeping Casco Bay alive and thriving.

For more information on the Friends of Casco Bay, visit the cascobay.org. The Cumberland County Conservation District also has a variety of ways you can support soil and water conservation efforts.

Also, the city of Portland’s stormwater runoff fee gives residents credit for reducing the amount of stormwater runoff from their property.