Editor's Note: The Thames River begins in Norwich and, 15 miles later, empties into Long Island Sound. It's very much a working river, with diverse industry on its banks, but it's a playground as well for boaters and beachgoers. The Thames is a river that helps shape our daily lives, but one we sometimes forget. This story is part of an ongoing series about the river. Find more at www.theday.com/thamesriver.

To the fishermen dangling poles from the docks at Norwich's waterfront park, the small craft making loops in the harbor all day with Howard "Mickey" Weiss at the wheel might have seemed to be on a very curious kind of cruise.

But for Weiss and his three-person crew, the "research cruise," as he calls it, was all about satisfying curiosity of the scientific kind, rather than rousing it.

Weiss and the crew came from Project Oceanology and the University of Connecticut at Avery Point, which share a campus along the river and are working together on this project to expand the understanding of the Thames River system.

"We've been out here since 7," said Weiss, senior scientist and founder of Project O, the marine science education program, a little before 11 in the morning one day last week. "We're taking measurements through the whole tidal cycle."

Technically an estuary, or tidal finger of Long Island Sound, the Thames "is really more akin to a fjord" than a traditional river, Weiss noted, and Norwich harbor, though very deep, doesn't act like a mixing bowl where the salt water from the Sound combines with the fresh water from the Yantic and Shetucket rivers.

Instead, it's more like a traffic circle with two lanes separated by a median, where the bottom channels the salt water that travels 16 miles upstream from the river's mouth, the top channels the fresh water, and the two rub shoulders in a narrow middle zone.

"It all looks the same, but when you go and measure it, you find there are really discrete layers," Weiss said. "The bottom 10 meters of Norwich Harbor is really Long Island Sound."

The Thames, he continued, "is a very important lab for Project O. We're on the Thames daily with our students. What a wonderful classroom for showing them how an estuary works."

Hypoxia is a concern

With silver hair and a teacher's knack for explaining concepts such as dissolved oxygen and hypoxia, Weiss steers the Project O boat with an ease acquired over more than 20 years of plying the Thames to take its pulse through its chemistry. Over those years, by tracking water temperature, salt and oxygen content and dissolved oxygen percentage at various depths at 14 locations from New London to Norwich, he's documented a troubling phenomenon that occurs each summer.

In June, the bottom two-thirds of Norwich harbor turns hypoxic, with oxygen levels so low "it's pretty devoid of any animals whatsoever," he said. If it had adequate oxygen, creatures such as clams, worms and small crustaceans called amphipods would be living in the sediment muds.

As the summer progresses, the hypoxic zone expands south as far as Allyn's Point in Ledyard, and creeps higher into the water column, forcing any marine life into the narrowing band near the top. Then in the fall, as the temperature cools, the condition gradually recedes until it disappears entirely, even in Norwich harbor where it was at its worst.

The occurrence of hypoxia each summer is a concern, he said, because it means the river can't support the entire array of marine life that it should, and that it's bearing the burden of human pollution.

The state Department of Environmental Protection categorizes the Thames as one of the state's "impaired" rivers, meaning it doesn't meet federal standards on one or more measures. The federal Clean Water Act requires the state to take steps to improve such waterways.

"We know there are ongoing water quality problems in the Thames River basin," said Eric Thomas, environmental analyst for the DEP. "We're slowly chipping away at it. It's a very large and complex watershed, and we're trying to determine where to put our limited resources to best use" to address the problems.

Six municipal sewage treatment plants in Connecticut empty into the Thames between Norwich and New London, and another half dozen industrial plants, including the AES Thames and NRG power plants in Montville and Electric Boat in Groton, discharge wastewater into the river.

Mostly, the discharges over the past year have met limits set by the state for levels of pollutants allowed in the wastewater, said Melissa Blais, DEP senior sanitary engineer, although there have been occasional violations. Most notable was a day in January when a discharge from EB proved highly toxic to creatures used to test the discharge water quality.

Upgrades in recent years to the municipal sewage treatment plants, funded largely with state or federal grants, have enabled them to release cleaner water more consistently into the river, though there are still further improvements to be made, Thomas said.

In particular, the Norwich plant, an aging facility that discharges near the harbor, overflows after heavy rains and ends up releasing bacteria-laden untreated sewage. In April, the city approved $40 million worth of upgrades to the plant over the next five years, which should improve the quality of the water it discharges. It will take another $40 million, however, to fully correct the storm water overflow problems.

"It's a working river, with a tremendous number of complicated uses," said the DEP's Thomas.

Many sources of pollution

The river's most difficult water quality problems appear to originate beyond where the Thames officially begins at Norwich harbor. The Yantic and Shetucket that converge into the Thames are in turn fed by a sprawling network of lakes, streams and rivers including the largest, the Quinebaug, over a 1,478-square-mile watershed that covers a third of Connecticut and stretches into Massachusetts and Rhode Island.

Aging sewage treatment plants empty into feeder rivers in northeastern Connecticut and Massachusetts, and polluted runoff from farms, lawns, septic tanks, roads and parking lots spills freely downstream and ends up in the river.

In essence, it's the "non-point source" pollution issue that plagues many watersheds nationwide - many small polluters all adding up to a big problem.

"It's a universal issue when you develop land," said Jean Pillo, who works on water quality issues throughout the watershed in positions with the Eastern Connecticut Conservation District, the Thames River Basin Partnership and The Last Green Valley, a nonprofit that promotes preservation and appreciation of the region's resources.

"There has been a general lack of knowledge that there are water quality problems, and how to get people to accept that they're part of the problem," she said.

Dams part of the problem

The U.S. Geological Survey, in a 2005 report, noted that the particular way the region developed historically made it more prone to the "significant" water quality problems. Even though the watershed is more than 75 percent forest and wetlands, mill villages and urban centers grew up along riverbanks, so polluted runoff scurries directly into the waterways rather than first getting filtered and cleaned through woodland soils.

The many dams throughout the watershed - some the legacy of the textile industry that built the region's mill towns, others built for flood control or power generation - compound the problems. Water, rich with nitrogen, phosphorous and other nutrients from sewage, fertilizer, pet waste, detergent residues and other sources, flows in and gets impounded at the dams. There, the nutrient-rich water warms, creating the ideal environment for excessive algae growth in the summer.

When the water is released from the dams, the algae flows downstream and ends up in Norwich harbor, where it dies when it meets the salt water. Weiss has surmised that as the algae decomposes and sinks, it consumes much of the oxygen in the salt water from the Sound and the fresh water from upstream, causing the hypoxia.

"Our hypothesis is that the water stagnates in the deep hole" in Norwich harbor, he said. "There isn't a chance for the bottom waters to be replenished, and with so many nutrients falling into the sediment and decomposing, it creates an oxygen demand."

More monitoring needed

To confirm his theory, Weiss has teamed with Michael Whitney, assistant professor of marine sciences at Avery Point, to measure the currents in the harbor. That will tell them whether the stagnation is indeed occurring and leading to the hypoxia.

Last week, aboard a Project O boat with Weiss and Whitney, maneuvering instruments in and out of the dark water and recording data on clipboards, were Ivan Otterness of Ledyard, a Project O volunteer, and Michelle Slater, an undergraduate marine sciences student at Avery Point.

"This is naturally an area that would be likely to have low oxygen," said Whitney, checking readings on a Panasonic Toughbook connected to data collection instruments as Weiss steered the boat to the next sampling spot in the harbor. "The fresh river waters are literally floating on top of the dense salt water from Long Island Sound, and capping them so they can't get to the top. But it seems the nutrients we're adding are exacerbating the situation."

Understanding the mechanisms creating the hypoxia is one challenge. Finding and correcting the sources is another, perhaps more difficult one. Because the non-point pollution problem, by definition, comes from multiple small sources, many individual projects are required to fix it. Farmers are being asked to manage silage and manure better, to avoid nutrients getting carried away with rainwater. Graywall Farms in Lebanon, Pillo said, is one being cited as a model for its management practices.

Thomas cited a demonstration project to reduce polluted runoff from UConn's main campus in Storrs and the town of Mansfield into Eagleville Brook. It recommends using porous materials instead of asphalt for parking lots to let storm water penetrate into the soil, wetlands restoration and drainage improvements, among other steps.

The DEP is also beginning work with towns to better manage storm water, Thomas said.

Other examples, Pillo said, include a rain garden project in Woodstock and a bit of water quality detective work she's begun this summer on Mashamoquet Brook. The stream feeds a popular swimming area at a state park in Pomfret that closes for at least a few days most summers because of high bacteria levels.

Every Thursday morning for the past two weeks, Pillo has set out before 7 a.m. to collect water samples from 16 spots on the brook. She delivers the samples to the regional public health agency offices, where a courier picks them up for delivery to the testing labs at the state Department of Public Health in Hartford. By the end of the summer, she hopes, she will have enough data to identify the source or sources of the contamination. Then she'll work with the town's conservation commission on a correction plan.

"There's not enough time for the DEP to do all the sampling itself," she said.

Other efforts to address the water quality problems are coming from The Last Green Valley, in the form of public education and awareness campaigns and its "Source to Sea" project last year. Volunteers have been used to collect water quality and habitat information.

But much more monitoring of the many waterways in the Thames watershed would be needed to really pin down as much as possible the specific sources of the pollution, and what corrective actions could be taken.

All the separate projects are aimed at the same goal - cleaner water throughout the watershed - but there is no overall coordination, Pillo and others said.

"There is no big Thames River watershed plan," she said.