PORTLAND — Joe Payne’s initial impression of Casco Bay’s health in 1991 was better than what he expected.

But a month before he retires after 24 years as the first – and only – Casco Baykeeper for Friends of Casco Bay, he said he still worries that water health will become worse than people might imagine.

“Nitrogen is our newest threat,” Payne, 67, said Monday, noting its accumulation in Casco Bay ultimately leads to low oxygen conditions and acidification of clam flats.

“If they can move, they move. If they can’t, they die,” he said of the marine wildlife affected by increased nitrogen flow, which can create algae blooms that eventually turn oxygen to carbon dioxide when broken down by microorganisms.

A Portland native, Payne became baykeeper in 1991, a position created by the nonprofit Friends of Casco Bay in part as a reaction to a 1989 report labeling the bay as one of the most polluted in America.

He said he soon discovered the dire report was flawed, because it measured toxins in the liver of a flounder that was not caught in Casco Bay and lacked other data needed to establish the bay’s health.

“(Casco Bay) was actually in pretty good shape, though there were some problem areas like Portland harbor and Back Cove,” Payne said. “I’m not comfortable answering the question the same way now.”

Payne’s return to Portland came as “waterkeepers” were becoming established to steward the health of fresh and saltwater environments, including the Hudson and Delaware rivers, San Francisco Bay, and Long Island Sound. He became the seventh such waterkeeper in the world.

Payne had been working as a marine biologist and living in New Hampshire when the Friends advertised the position. Because his work took him throughout New England, he said it led to a piecemeal approach to protecting watersheds that was not always rewarding.

“Those were disparate efforts, a little bit here, a little bit there,” he said. “This was in my field and focused on the place I loved.”

But he hesitated to respond to the ad because his wife, Kim, was also a marine biologist, a position not always in demand in Maine.

“Maine has 5,400 miles of coast and no jobs for marine biologists,” he quipped.

But encouraged by his wife to apply, Payne said he was energized because he was focusing on one body of water.

“At first, it was such a relief of just having Casco Bay,” he said. “Then I realized how big it is and how many problems there were.”

Making Casco Bay more visible, to make it more treasured, was a first step to getting at problems of pollution. But Payne said the approach has always been as much about economics as conservation.

“We have never had a kind of lock-it-up-(and)-preserve-it mentality,” he said “We want people to use it. It is an economic driver.”

Wider use and understanding of bay conditions led to enlisting volunteers to test the water, a program that has now drawn about 650 people. Dissolved oxygen test results are considered a primary indicator of the bay’s health.

“If something is going on in the water, you see it in the oxygen, high or low,” Payne said.

Increased testing led to reopening long-closed clam flats the state lacked the resources to re-evaluate, and for the relocation of 35,000 lobsters from Portland harbor before a channel dredging in 1998.

The threat now is from watersheds as far north and west as Bethel, Payne said. About a third of the nitrogen now threatening the bay is runoff from sources including fertilized lawns on private properties, he added. In 1998, the Friends began its “Bayscaping” program, designed to discourage property owners from using pesticides and fertilizers while still growing lush lawns.

Other nitrogen is airborne, or leaks from water treatment plants not equipped to handle the element, he said.

Along with oxygen depletion, excess nitrogen can cause acid levels to increase in sediments, a condition that destroys the developing shells of shellfish larvae known as spats.

Payne estimated the value of a harvested clam increases by a factor of four as the clam makes it way from the flat to the kitchen.

“A good environmental decision is 100 percent of the time a good economic decision,” he said.

Payne said his most harrowing days came in when the oil tanker Julie N struck the old Casco Bay Bridge on Sept. 27, 1996.

“You feel helpless when there is 180,000 gallons of oil on the bay and leaking into the bay. It was devastating to people’s psyche,” Payne said.

He credited quick, well-rehearsed containment practices set up by the U.S. Coast Guard about five years before the spill, and a commitment from the tanker owners to clean first and assess fault later, with a successful 78 percent removal of the oil.

“We think it was a world record, but we didn’t call the people at Guinness,” Payne said.

Other measures Payne advocated to sustain the health of Casco Bay include municipal efforts in Portland and South Portland to separate storm and waste water flows, and prohibiting cruise ships from dumping waste water in the bay.

While he plans to spend more time with his wife at their Peaks Island home, Payne will not sail quietly into the sunset. He will have the new title of Casco Baykeeper Emeritus, and said he looks forward to volunteering his time for a new baykeeper.

Friends of Casco Bay is encouraging the public to share memories of Payne by Dec. 19 in email to slyman@cascobay.org, and is welcoming donations to a new Emeritus Fund established in Payne’s honor.

Payne will also be honored at a public celebration on Jan. 21, 2015, at DiMillo’s on the Water, 25 Long Wharf.

David Harry can be reached at 781-3661 ext. 110 or dharry@theforecaster.net. Follow him on Twitter: @DavidHarry8.

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Joe Payne will retire next month after 24 years as the Friends of Casco Bay baykeeper.