Wagging their wide tails as Kait Maginel and David Prescott tossed them back overboard, two lobsters that had shared a wire trap overnight with four spider crabs and a whelk had just been enlisted as ambassadors in the cause of cleaning up the lower Pawcatuck River and Little Narragansett Bay.

"There's still a lot of great life here," Prescott, South County coastkeeper for the nonprofit environmental advocacy group Save the Bay, said Thursday. "This is why we want to protect it."

Prescott had just shown the shellfish to an audience of those who share the waterway — officials from Westerly and Stonington, as well as state environmental regulators from Connecticut and Rhode Island. Save the Bay had gathered the group aboard its educational and research vessel Elizabeth Morris that morning for a two-hour tour of the estuary designed to reinforce its "call to action" for the two states, two towns and other towns upriver to collectively improve the water quality in the lower river and bay. There, saltwater from the Atlantic mixes with freshwater from the 300-square-mile Wood-Pawcatuck watershed that extends into 10 towns in Rhode Island and four in Connecticut.

But instead of being a healthy estuary rich with edible shellfish and a diversity of marine life, much of the lower river and bay are, in effect, sick. The diagnosis includes changing patterns of marine and freshwater flows, but is primarily eutrophication — an overload of nitrogen-heavy nutrients pouring into the waterway, causing large sections to become a monoculture of nuisance algae.

In essence, the lower Pawcatuck and bay are like an overweight person who continues to ingest excess calories with no means of flushing them out through exercise.

"The nitrogen load is definitely fueling this problem," said Jamie Vaudrey, assistant research professor at the University of Connecticut, who has studied the estuary and others along Long Island Sound. "There are so (many) nutrients entering this system, it's fueling this huge biomass."

The "huge biomass" is cladophora, a nuisance algae that is taking over an area once dominated by eelgrass, a marine plant that provides habitat for many sea creatures and indicates good water quality. Maps she created show cladophora, a stringy, opportunistic algae that entirely covers the bottom in large swaths of the estuary, growing in mats 3 feet thick in some areas.

"Over the last 15 years, there's been a rapid loss of eelgrass, replaced by cladophora," she said. In addition to the nitrogen-laden runoff, cladophora is also thriving in recent warmer winters due to climate change, she said, and reduced flows of marine water as the bay and lower river get pinched by the northwest drift of the Sandy Point barrier beach. Prescott said Sandy Point has moved 300 to 400 feet during the last 45 years.

"When we did dive surveys out there, it was like being in a creepy Halloween forest of 2 to 3 feet of algae in some places," he said.

Karen McGee of Stonington borough finds cladophora's takeover of the estuary revolting for other reasons. From the backyard of the home she moved into two years ago, she looks out over Ash Street beach, a sandy strip she wishes she and others could use as a kayak launch and swimming area. Instead, it's covered with a dense mat of dead eelgrass and other algae that has washed up and gotten trapped there. Anyone who steps too far out onto the mat sinks in up the knees in black ooze. Essentially, Vaudry said, the beach has turned into "a giant compost pile." As the cladophora kills off other marine plants, and dies and decays itself, it all washes up on the Ash Street beach on the eastern side of the borough.

After the noxious smell from the decaying seaweed became intense in 2012, causing some neighborhood residents to complain of headaches, borough officials had it trucked away. Not long after, though, the beach was again completely covered.

"We paid $10,000 to have it carted away in 2012, and $6,000 in 2013 and 2014, but of course the stuff came back," borough Warden Jeff Callahan said. "We can't keep spending that kind of money to clean up 100 feet of shoreline. It's unsustainable. But we haven't found a solution yet."

Last year, McGee helped form the Coalition for the Management of Seaweed in Stonington, bringing together town, borough and state environmental officials with borough residents to understand and brainstorm solutions to the problem. A marine engineering firm developed proposals to create an incline on the beach to prevent seaweed from accumulating, and suggestions for seaweed traps offshore were considered. But thus far, no cost-effective practical solution has been found.

"People complain about it, but we're not making a lot of progress," McGee said. "We're all kind of stuck."

She understands that the seaweed accumulation is the symptom of larger problems in the lower river and bay, and that remedies are likely to take years to implement.

"It's not just that we want a usable beach," she said. "We also want the bay to be healthy."

Prescott said seven years of water-quality monitoring by Save the Bay have documented that the lower river and bay have elevated bacteria levels, high levels of nitrogen-rich nutrients, poor flushing and decreased levels of dissolved oxygen needed by marine life. In the "call to action" he and others from Save the Bay issued Thursday, local and state officials were urged to work on several areas: stormwater management; stricter enforcement of septic system regulations, better enforcement of no-discharge zones for boats; promoting natural buffers of vegetation around waterways; and continued water-quality monitoring.

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They called on the public to do its part by reducing the use of fertilizers and pesticides, cleaning up pet waste and not feeding waterfowl. Prescott and others also cited the need for a water circulation model to be done of the lower river and bay so there's a better understanding of how the incoming tides are mixing with freshwater from the river.

Because of urban development of the lower watershed, he said, the river and bay essentially become the receptacle of all the pollutants that end up on streets and parking lots. On a rainy day, the many discharge pipes for untreated stormwater that empty into the river deposit trash, grass clippings, fertilizer and pesticides, oil and gas and other pollutants along with rainwater.

"As far as I'm concerned, stormwater is the single most important issue there is," said Claire Gavin, former director and volunteer for water testing with the citizen group Clean Up Sound and Harbors. The Stonington-based CUSH has conducted its own water-quality testing and has run programs encouraging residents to curb use of fertilizers on lawns. "What comes out of those storm drains is very destructive. But there is a sense of defeat, that you can't do anything about stormwater."

In addition to the stormwater discharges, the lower river and bay also receive about 3 million gallons per day of treated wastewater from the Westerly and Pawcatuck sewage treatment plants. But Prescott and others believe the plants are not a main source of the problems, citing recent equipment upgrades that have improved removal of bacteria and nitrogen from the wastewater. According to Heidi Travers, senior engineer with the Rhode Island Department of Environmental Management, the two treatment plants empty up to 176 pounds of nitrogen into the estuary daily, about one-tenth of the amount coming in with the freshwater discharges from the river.

The Westerly plant is the larger of the two, discharging an average of 2.4 million gallons of treated wastewater daily containing about 138 pounds of nitrogen, said Joseph Haberek, principal sanitary engineer for R.I. DEM. The Pawcatuck plant discharges about 500,000 gallons of treated wastewater daily, containing about 15 to 20 pounds of nitrogen, said Tom Gilligan, director of the Stonington Water Pollution Control Authority. The discharges from both plants fall far below the nitrogen limits set by their respective states.

There is also a smaller treatment plant in Stonington borough, but it discharges in another area and is not considered to be a factor.

Despite that, Vaudrey believes the estuary would benefit greatly if nitrogen discharges from the two plants were brought even lower. By her calculations, 69 percent of the nitrogen in the waterway is coming from the treatment plants. Fertilizer is the next largest source, at 16 percent, and stormwater accounts for about 13 percent, she said. The remaining 2 percent is from septic tank runoff.

"My suggestion is that the limits (on the plants) aren't stringent enough," she said. "The technology is there to recycle nitrogen nutrients into compost, but instead we're taking nitrogen and pouring it into the ocean."

j.benson@theday.com

Twitter: @BensonJudy