NEWARK, N.J. - What exactly is that black goo in water sample No. 242807? And how did it come to be in the Passaic River on a recent Friday afternoon under the Pulaski Skyway just as Kelly L. Rankin and her team happened by in the Phoenix, their 25-foot research boat?

Rankin, an assistant professor at the Stevens Institute of Technology in Hoboken, is the first to admit she does not have the faintest idea.

Yet.

It is audacious to even think that she could know how any one corner of the sprawling, sloshing, wind-tossed system of bays, inlets and rivers that constitute the New York Harbor estuary really works. But that is the goal.

It's all about mud. Over the next decade, millions of tons of the harbor's silt, sand and muck - much of it contaminated by decades of industrial pollution - must be dredged to keep the port competitive.

Knowing what's in that mud, how it moves and where the pollutants come from, could save hundreds of millions of dollars, the experts say, by reducing disposal costs - since cleaner sediment is cheaper to get rid of - and by preventing more pollution from fouling the harbor.

A computer model

The mechanism for the work is a computer model that, when completed by the end of next year, using data collected by Rankin and others, will provide what engineers say will be the most sophisticated analysis ever of how a harbor system actually works.

Even one of the simplest parts of the program, learning how water flushes over the course of a year through the interconnected water systems from Long Island Sound to the East River and up the Hudson, requires a computer to grind through 7 million equations. It gets really complicated after that, when factoring in things like sediment flow and the 300 or so different pollutants in these waters.

"At first, people think we're crazy to undertake this. Then they're interested," said Michael Bruno, the director of the Davidson Laboratory at Stevens Institute and an investigator for the project, which includes researchers from more than a dozen universities and government agencies.

The pressure to succeed is enormous. Over the next decade, the Army Corps of Engineers will dredge more than 65 million cubic yards of silt and sand from the estuary to make room for a new generation of supercargo tankers that ride deeper in the water.

If the harbor is not dredged, the big tankers will take their business elsewhere, port officials say, costing the region hundreds of millions of dollars in lost revenue and thousands of jobs. But because much of the mud is polluted with everything from dioxins to heavy metals, disposing of it is also extremely expensive, up to $50 per cubic yard, and in some cases even more. One recent pilot waste-disposal project, using harbor mud to seal up old mine shafts in Pennsylvania, cost $70 a cubic yard.

Confluence of interests

The estuary research effort, known by its acronym, CARP (Contaminant Assessment and Reduction Project), was thus born of a rare confluence of interests. Environmentalism and hard-nosed economics have aligned. Basic scientific research, sometimes criticized as a boondoggle that wastes public money, has been enlisted to save a buck.

"This is one of those situations where the costs of contamination are being borne not only by the environment and the public but also by a specific economic sector, one that's facing enormous competitive challenges," said Bradley M. Campbell, commissioner of the New Jersey Department of Environmental Protection. "The toxics-tracking program will help ameliorate both the environmental impacts to living resources and the economic impacts to the port."

Getting a better sense of how pollutants and sediments move around in the system, Campbell and other officials say, might allow dredging engineers to clean up the dirtiest spots first or the spots where sediments are concentrated by tidal or wind action, and so avoid doing the same channel twice.

"It's like raking the leaves - you don't want to come back the next day and do it again," said Joel Baker, professor of environmental chemistry at the University of Maryland and chairman of a group of scientists advising on the computer modeling.

Other scientists said the vast details, like dividing the water from Cape May to the tip of Long Island Sound into a three-dimensional grid of 26,000 cells, each trackable by the computer model, have become part of the project's dizzying charm. And they freely admit they are making it up as they go along.

"We're one of the few places looking at this, so we've had to develop our own answers," said Tom Wakeman, the general manager for waterways development at the Port Authority of New York and New Jersey.

Sophisticated models of ecological phenomenon are not new. But scientists and government officials say the project, which has already cost $20 million, most of which was provided by the Port Authority, is so ambitious because it has to be.

It is partly a matter of scale. Officials at the Port Authority, which manages the harbor, say they think that if the program succeeds, the costs of dredge disposal might be cut in half to $25 per cubic yard or less. Spread over millions of cubic yards, those savings will add up fast.

The harbor system is also intensely complicated in ways that researchers are only beginning to understand. In the past, for example, scientists were much more likely to focus on storms as explanations of how sediment and contamination moved. Through the CARP research, they have found a kind of feedback loop that mainly seems to hinge on wind in places like Raritan Bay, south of Staten Island.

When strong winds blow from the east, the bay's shallow waters are driven in toward the New Jersey coast. But when the wind shifts back to the west - especially if its speed exceeds what appears to be a trigger point of 27 knots - the surge of pent-up water creates a kind of vacuum that drains water from other sources, including Newark Bay and the Passaic River.

Part of the accumulated pollution in the Kill van Kull, the channel separating Staten Island, N.Y., and Bayonne, N.J., for example, might not be from the industries along the channel's banks, but from factories or sewage plants miles away, drawn by the flushing action.

New sets of questions

Elsewhere, the research is revealing mysteries that pose whole new sets of questions. In some samples from waters near Staten Island, for example, scientists picked up traces of DDT, the insecticide that was banned in 1972. What perplexed them was that the chemical had not been broken down or weathered by long exposure to the environment. That suggested a leak, perhaps from a land-based source that had not been identified.

"We're in a new battlefield; we now have to find where these leaking drums are," said Dr. Dennis J. Suszkowski, the science director for the Hudson River Foundation, a nonprofit group that is overseeing part of the CARP work.

Suszkowski says he thinks that, sooner or later, politics will have to pick up where the scientific investigations leave off - and how that might be resolved is also a mystery. If and when other trails in the project lead to other specific land sources, will there be enough political will to go after offenders? "It becomes a societal issue then," he said.

For Rankin, the fieldwork has meant days on end aboard the Phoenix, many of them in the worst weather conditions, the better to gather data. And she acknowledges that many of the urban seascapes of New York Harbor and Newark Bay are gritty and decayed. Jacques Cousteau country it is not.

"People think oceanography, they think Cape Cod and Woods Hole," Rankin said as the Phoenix pushed north near the New Jersey Turnpike. "But I love it here. This is where the gritty, good issues are."