The URI School of Oceanography research vessel Cap’n Bert returns from its weekly trawl survey. Data from the trawls is used to evaluate the health of Narragansett Bay.

The Providence Journal / Andrew Dickerman

On a warm fall morning just east of Wickford Harbor, steel cables on the research vessel Cap’n Bert whir as a winch pulls aboard a 20-foot net that the vessel towed for half an hour along the bottom of Narragansett Bay.

As the net rises onto the gallows frame straddling the vessel’s stern, Anna Malek, a University of Rhode Island graduate student, pulls the puckering string and a flopping, sputtering mass of fish splatters onto the deck.

Malek and fisheries scientist Jeremy Collie bend over the pile and begin culling fish into orange buckets. Soon, it is clear that their catch is very different from what fishermen would have caught even as recently as 10 years ago.

They count 1 bluefish, 8 tautog and 15 flounder. But they also find 11 mud crabs, 1 cancer crab and 8 starfish. They pick up dozens of brown globs that they throw onto a pile that grows to be about half of what they caught. The ugly creatures are tunicates or sea squirts, an invasive species that covers much of the ocean bottom throughout the Northeast.

Their catch also includes 608 scup and 35 moonfish, fish that used to be unusual in Rhode Island waters.

The trawl is part of a unique scientific survey that has gone on as long as any other fish survey in history — once a week for 50 years in this stretch off Jamestown and another at the mouth of Narragansett Bay.

It reveals what is obvious only to fishermen — dramatic changes in life in the Bay.

Collie, in a paper published last year in the Canadian Journal of Fisheries and Aquatic Sciences, says rising sea surface temperatures of nearly 3 degrees Fahrenheit in 47 years are a primary cause of the changes. Studies show that even slight temperature changes over long periods of time directly influence the composition and abundance of fish species. Fishing has had a secondary effect, he said, causing the average size of fish to be smaller.

Marine life in the Bay has moved from primarily vertebrates (fish) to invertebrates (crabs, squid and lobsters). And especially since 1980, it has also shifted from bottom dwelling fish such as flounder and hake to so-called pelagic fish that swim higher in the water — menhaden, bluefish and stripers.

The winter flounder and other bottom dwelling fish that used to provide a major source of income to local fishermen have been replaced with inedible crabs and sea squirts. Some call it the “crabification” of the Bay.

THE CHANGES offer a complex message to those who care about the Bay.

On the one hand, they are evidence that climate change is triggering ecological changes. And the changes are even more frustrating because they are occurring as the state attempts to become a national leader in how it manages the Ocean State’s waters — an effort that has been slowed to a crawl by the state’s financial woes that have prevented state agencies from launching new efforts to reduce pollution.

At the same time, sewer authorities and their rate payers have continued to invest heavily in cleaning up coastal waters — an investment that is producing what some see as historic improvements in water quality.

Last year, the Narragansett Bay Commission put into service its $359-million combined sewer overflow system to capture storm sewer overflows. There were immediate indications that it has improved the Bay’s water quality and reduced the frequency of shellfish bed closures.

Recently, the state loaned $135 million to local communities for water projects, with most of the money going to sewer plant improvements, many aimed at reducing flows of nitrogen into the Bay.

Also, habitat restoration projects such as dam removals and salt marsh restorations are under way around the Bay.

“We’re doing the best we can, considering the scarcity of resources, the legacy of pollution and climate change,” says Ames B. Colt, chair of the Rhode Island Bays, Rivers, and Watersheds Coordination Team, which includes top officials from seven state agencies. “Ecology has become the dismal science. There’s not a lot of good news.”

The lifetime of the trawls has coincided with unprecedented efforts to reduce Bay pollution. Through the state’s efforts, the Providence sewage treatment plant was transformed from one of the country’s worst to the best. Hundreds of millions of dollars have been spent on other sewer plant upgrades.

The jewelry industry was ordered to stop dumping toxic metals into the Bay.

There has been a steady decline in the heavy industry that once contributed vast amounts of pollution.

Still, there have been troubling signs.

The interaction of warm water, low tides and low oxygen conditions caused a massive fish fill in Greenwich Bay in August 2003.

The fish kill raised public concern and prompted a forceful reaction from the state’s political leaders.

They passed a suite of new laws, praised by oceanographer Bob Ballard, that called for “ecosystem-based management” — a concept that means different things to different people but boils down to trying to manage the health of an entire ecosystem rather than continuing the traditional path of separately regulating fishing for each species of fish without regard to the rest of the environment.

One example is the two-year, $4-million effort to plan the location for Rhode Island’s offshore wind farm. Scientists are assembling unprecedented volumes of data by doing studies of fish, birds, mammals, fishing, transportation and climate change to try to avoid putting the giant turbines in the wrong place. Most regulatory decisions are based on far less science and data.

The new ecosystem management plan is supervised by Colt’s coordination team. And it did enact a five-year plan this year with a series of goals. But ask Colt how far the new management program has proceeded, and he says: “Not very far at all.”

The goals come with no firm numbers, he said. “The agencies didn’t want to hold themselves to hard targets because of concerns about resources. Hard targets require extraordinary commitment.”

“We have to take a more unified approach to somehow manage the Bay as a system,” says Colt.

“We recognize that though we control fisheries effort and water pollution as much as we can and we’re doing habitat restoration — despite all our good efforts in those separate spheres — we’re still seeing the crabification of the Bay. Even though we are doing a lot better on a lot of fronts, we’re still seeing negative human effects [on local water bodies], plus there’s climate change.”

Some observers are more positive.

John Torgan, baykeeper for Save The Bay, is out on the Bay all the time and he says he sees improvements.

“I think we are in better shape than we’ve ever been before,” Torgan said.

“Despite record rainfalls this summer, we saw fewer beach closures,” said Torgan. “That’s big news.”

He says he’s seen the return of vast schools of menhaden, more ospreys, more stripers, more bluefish and oysters. The water looks good in the upper Bay and there’s much less garbage on the shores.

It’s only one year, but Torgan said he didn’t get a single call this year about stinking piles of seaweed or dead clams on the shore.

He’d like to see more of the upper Bay opened now to swimming and shellfishing. Unfortunately, he said, state regulatory agencies don’t have the resources to collect the information to justify the openings. The state is raising new funding through fees imposed on the disposal of septic wastes. It also gets money from the state’s oil-spill cleanup fund. But another major monitoring project, separate from the URI trawl, is at risk.

Colt says the state’s congressional delegation reports that $750,000 in federal funding could be cut next year, killing the Bay Windows monitoring program operated by the National Oceanic and Atmospheric Administration. The program was initiated by the late Sen. John H. Chafee in 1997, the year after the North Cape oil spill. It funded a state research vessel and a system of buoys and surveys that track ecological, chemical and physical conditions in the Bay.

He says he keeps pushing the new, five-year plan and trying to educate people about the health of the Bay.

“The painful parts of the story we tell are not easy to accept,” said Colt. “Life is expensive. You will have to pay for things you enjoy.”

“The complexity of what we are dealing with is often unclear to the public.”

LAST MAY, 50 scientists and resource managers met at Roger Williams University to discuss a report on the status and trends of the Narragansett Bay region.

The report’s key finding was that the Bay has undergone “significant environmental improvements in recent years” and the new combined sewer overflow in Providence and improvements to sewage treatment plants around the Bay reduced nitrogen discharges by one third and also reduced contamination of beaches and shellfish beds.

But the group also found pollution from storm water, cesspools and failed septic systems continues to cause “major impacts” on water quality and continued development around the Bay is worsening storm water runoff.

Finally, the scientists agreed that environmental information is of variable quality and coverage, making it “difficult to assess ecosystem trends or determine the effectiveness of environmental management.”

The URI trawl continues to be the one monitoring effort that has not wavered. It was started by Charles Fish, who with his wife, Marie, established the University of Rhode Island’s first marine biological program in 1935. They later developed a graduate program in oceanography at the Narragansett Marine Laboratory and it evolved into URI’s Graduate School of Oceanography.

The initial purpose of the survey was to track migratory fish. Later, scientists agreed it was a valuable source of data about fish populations and water temperatures.

For 30 years the survey was operated by H. Perry Jeffries, an emeritus professor, as well as countless graduate students. Jeffries once gave temperature data to engineers designing the Jamestown Verrazzano Bridge — they needed to know the temperatures on the bottom of the Bay when mixing and pouring concrete. Ten years ago Jeffries turned the survey over to Collie. In 50 years, 1.8 million fish were counted.

MALEK AND COLLIE sort the fish as the Cap’n Bert heads south under the Jamestown Bridge and slows at Whale Rock off Narragansett, where they will begin their second trawl. A half hour later, when the net is swung aboard, it is clear this trawl produces more fish than the one in the upper Bay.

Among the catch was an unusual find — a torpedo ray that weighed 10 pounds and was as wide as a doormat.

There was a good cross section of butterfish, flounder, hake and scup. But there were also 191 squid, 48 cancer crabs, 10 lobsters and 6 starfish. Fairly typical.

Collie said he used data from the URI trawls to support a major international report published this summer that finally offered some hope for the world’s fish populations — it found that when fish catches are sufficiently reduced, fish stocks will rebound even from extremely low levels.

“This trawl has had a global significance,” Collie says, as the Cap’n Bert heads back to Wickford. “It takes the pulse of Narragansett Bay as far as fish populations are concerned.”

The coordinating team’s five-year management plan and other documents can be found at www.dem.ri.gov/bayteam/index.htm.

To view Currents of Change, a report on the Bay’s condition prepared this year by 50 scientists and resource managers, go to www.nbep.org.The catch in early September off Fox Island:

plord@projo.com