CRANSTON — Katie DeGoosh leans over a concrete abutment alongside Reservoir Avenue and drops a line with a white, Teflon bucket into the clear waters of the Pocasset River. It flows almost unseen through this neighborhood jammed with gas stations, fast-food restaurants and medical buildings.

DeGoosh, a biologist, and Kristen Chantrell, an engineer, both at the state Department of Environmental Management, pull the bucket up to the street and pour the river water into bottles and jars to be analyzed for metals, such as zinc and copper, several kinds of nitrogen, acidity and other indices of pollution.

The river looks clear. But DeGoosh says it has been so long since this tributary to Narragansett Bay was tested, she has no idea whether it is clean or dirty.

The days of not knowing what flows into Narragansett Bay appear to be coming to an end.

In a period when the Bay’s marine life is undergoing dramatic changes, the manner in which state regulators manage the Bay is also evolving.

Public outrage over the historic fish kill in Greenwich Bay in the summer of 2003 led to studies that concluded too many nutrients were flowing into the Bay from many sources. The state ordered communities to upgrade their sewage-treatment systems at a cost of millions of dollars. The outrage also caused scientists and regulators to develop a new system for managing Narragansett Bay.

But it has all come slowly.

Despite the fact that nearly every state politician supported the Bay cleanup, progress has been delayed by political squabbles between the governor and the legislature over financing and personnel and the state’s financial crisis.

Those involved insist there is progress — at least in the scientific and regulatory efforts, if not yet in the Bay itself. And this winter there will be two major developments:

•State officials will present a new strategic plan for managing the state’s bodies of water, both fresh and sea.

•And Rhode Island-based scientists are publishing a book summarizing the last 25 years of science concerning the Bay. A key finding is that parts of the Bay function so differently from other areas, an eco-functional zoning plan should be created to better manage the bays within the Bay.

“We have found that the only constant about Narragansett Bay is change — and we’re in a period of accelerating change,” says Barry A. Costa-Pierce, director of Rhode Island’s Sea Grant program and co-author with Alan Desbonnet of the new book, Science for Ecosystem-Based Management — Narragansett Bay in the 21st Century.

“This is one of the best-studied bays in the world, and some of the surprises we’re finding are globally important,” says Costa-Pierce. The book finds that the Bay suffers from such health issues as regions of low dissolved oxygen and “a preponderance of opportunistic and nuisance species — weeds if you will — in the upper regions of the Bay.”

Some of that science points to new and disturbing ecological changes on the bottom of the Bay that may be triggered by global warming. The discovery has caught the attention of scientists around the world.

THERE WASN’T a politician in Rhode Island four summers ago who didn’t want to do something to improve the Bay and prevent further fish kills.

The slick of dead, young menhaden stretched 1.5 miles long and about 80 feet wide. It was the worst fish kill most local experts had ever seen.

A “perfect storm” of heavy rain that had carried nutrients into the Bay, followed by little wind and a hot, sunny day left much of Greenwich Bay with no oxygen. The lack of oxygen killed tens of thousands of fish and clams.

During the next session of the legislature, famed oceanographer Bob Ballard praised legislators for enacting six bills that he said were some of the most modern environmental legislation in the country.

The General Assembly also approved $19 million in bonds for projects to reduce water pollution and restore Bay habitat.

But in subsequent sessions, the legislature refused to ratify the governor’s choice to head the Rhode Island Bays, Rivers and Watersheds Coordination Team, the body that was supposed to revamp Bay management. And it twice cut financing for better water-quality monitoring.

Last year, at the height of his reelection campaign, Governor Carcieri convened a Narragansett Bay “summit” and announced plans for an $85-million bond issue for improving sewer plants and replacing cesspools — all to make Narragansett Bay the “cleanest estuary in the United States.”

The General Assembly did not approve the bond issue last session, but a Carcieri spokesman said he will resubmit the bond issue in the next legislative session.

Meanwhile, oceanographer Scott Nixon at the University of Rhode Island’s Graduate School of Oceanography, began talking about an analysis of the fish kill that did not lay the blame on worsening nitrogen conditions in the Bay. Nitrogen levels haven’t changed much in recent decades, he said. The fish kill, he said, was more likely due to an unfortunate confluence of wind direction, rain and currents.

Nixon is described by his peers as one of the best systems ecologists in the country. But most of the rest of the state’s scientific community, along with the legislature and governor, continued to demand a reduction in nitrogen from municipal sewer plants.

THE MOST surprising news about the Bay came last summer, with the publication in Nature, one of the world’s preeminent science journals, of new research by Nixon and Robinson “Wally” Fulweiler, a doctorate candidate at URI at the time.

They found an abrupt and dramatic reversal in the way bacteria at the bottom of the Bay deal with nitrogen. Instead of absorbing the nitrogen introduced by sewer plants, the runoff of fertilizer and other wastes, the bacteria were emitting additional nitrogen into the water.

“The [nitrogen] levels kept decreasing and decreasing, and then all of a sudden it switched,” Fulweiler said in an interview last summer.

The scientists concluded that in the summer of 2006, the bacteria added 1.5 times more nitrogen into the Bay than was introduced from sewer systems.

The finding is critical for at least two reasons.

First, in response to the fish kill, the state ordered local sewer departments to significantly reduce their nitrogen outputs at a cost of tens of millions of dollars.

Second, the scientists speculated that the new nitrogen production corresponded to a decline in the concentrations of chlorophyll in the Bay, which in turn could be a result of global warming.

Ames Colt, a former interim Sea Grant director who was finally approved to chair the watershed management team, says the DEM is required by the Clean Water Act to reduce nitrogen inputs that trigger low oxygen conditions in the Bay.

In response to Nixon’s findings, Colt said it is difficult to input “groundbreaking science into a regulatory system set up by the Clean Water Act.”

Colt continues preparing the new strategic plan that would lay out ways for various state agencies to better manage the state’s water resources.

“I am trying to make it as issues-based as possible, without being unduly controversial,” Colt said.

One technique is to set annual goals. He expects the plan will incorporate expected sea-level rise, ocean energy development, waterfront development and regional governance of coastal waters.

Colt says the timetable calls for setting goals for 2009 that would be reflected in the state budget of 2010.

“There is a lot of vision,” Colt says, “but not a lot of resources. We have a long way to go.”

THE CURRENT Bay management system sets pollution standards that may be imposed regardless of changing ecological conditions. The new ecosystem-based management system mandated by the state’s political leaders requires constant monitoring of water conditions so action can be taken in response to changes — much like using regular physical examinations and tests to monitor peoples’ health.

Sue Kiernan, deputy chief in the DEM’s water resources division, is charged with getting some monitoring done, despite having far less money than the DEM believes is necessary.

Last year, the General Assembly directed that $250,000 from the state’s oil spill response fund be used for monitoring. This year, the legislature agreed to a plan to raise more money through a tax on two transatlantic cables and on deliveries of septic wastes to sewer plants.

The DEM has used the money to reestablish streamflow gauges on some of the state’s bigger rivers and to initiate a series of samplings of tributaries to the Bay.

It sampled the Wood and Pawcatuck rivers, and then the Big, Flat and Queen rivers. This year, DeGoosh and Chantrell are spending six days collecting samples from the Pawtuxet and its tributaries.

“We’re reducing critical data gaps,” says Kiernan. “But we still have needs. We need more data to make permitting decisions.”

As for reducing nitrogen when some scientists, such as Nixon, suggest that is not the problem, Kiernan says, “Some people have referred to it as the grand experiment. We view it as a critical period of change.”

Some 1,500 scientists from around the country were at the Rhode Island Convention Center for the Biennial Conference of the Estuarine Research Federation last week. Costa-Pierce, Desbonnet, Nixon and Fulweiler all made presentations of their work and attended sessions hoping to learn from research on similar estuaries elsewhere.

Colt, who is in charge of the state’s Bay coordination team, wasn’t there. A DEM budget freeze leaves no money for such conferences.

plord@projo.com