INDIAN ISLAND – Last summer, most of Maine’s longest river was clogged with tiny balls of blue-green algae, giving it the color and texture of pea soup.

“Oh, it was bad,” said Jason Mitchell, water quality program coordinator for the Penobscot Indian Nation. “The algae was like little floating BBs all through the water.”

This week, as Mitchell made his regular rounds of sampling sites along the Penobscot River’s West Branch, the water was liquid gold.

“That’s about as good as it gets on the river,” Mitchell said, taking a measurement of the water’s clarity early Wednesday morning.

For more than 20 years, members of the Penobscot tribe have documented the slow restoration of their ancestral river, which for decades has been polluted by the loggers who used its course as a lumber highway and by the paper industry that grew up along its banks.

“The reservation is the river,” Dan Kusnierz, water resources program manager for the tribe, said this week.

Tribal holdings include 240 river islands, scattered between Milford and Mattawamkeag. The main reservation, at Indian Island near Old Town, is surrounded by water.

For centuries, Penobscots trapped and foraged along the banks and fished in the birch bark canoes for which the culture is known. Life revolved around the river. But today, tribal advisories warn pregnant women and children not to eat the river’s fish, which are contaminated with high levels of pollutants.

Carried along with the air pollution making its way northeast on the prevailing winds, mercury falls with rain, then undergoes chemical changes that allow it to build up in fish, wildlife and human bodies. In one impoundment on the Penobscot, mercury levels were higher than in samples taken downstream of the former Holtrachem manufacturing plant in Orrington, where mercury had been stored for years, Mitchell said.

While new technology has all but removed dioxins from paper mill waste, the toxic chemicals have accumulated in sediment over the years, making it nearly impossible to clean up.

Broad scientific studies to prove that Penobscots and other people who live along the river are suffering the effects of this pollution would cost hundreds of thousands of dollars. But the fatal cancer diagnoses that seem to increase every year have convinced many tribal members of the connection, including Penobscot Chief Jim Sappier and Mitchell, who started working in the water quality program after losing a friend to leukemia.

“It’s all bad news as far as fish are concerned,” Mitchell said. “I absolutely wouldn’t eat anything that came out of the river.”

Mitchell was raised in Old Town and grew up playing on the river’s ledges. Now he’s raising his own children here. He hopes that someday they can swim and fish in the river, knowing that it’s safe.

“The river’s got a long ways to go,” Mitchell said.

Every morning between May and October, Mitchell or one of his staff is up with the sun, loading well-worn scientific equipment into an aluminum boat to travel to a handful of 84 water sampling sites, which the researchers check weekly.

“We have the main stem of the river plastered with sites,” Kusnierz said.

In fact, the state Department of Environmental Protection has relied on the tribal research program for the past 10 years, ever since the state and the tribe signed a formal agreement to share information.

Penobscot data are used in the state water quality reports that biologists rely on to set policy, and tribal researchers alert state officials whenever they spot environmental law-breaking.

As the Penobscot River Restoration project, an effort to remove several dams and restore native migratory fish populations, goes forward, Kusnierz and his staff also will be in the perfect position to watch the river evolve.

“We have someone on the river every day, and we can be there and collect information very quickly,” Kusnierz said. “We’re sort of the eyes for the river.”

The relationship between the state and the tribe has been strained in the past, particularly a few years ago when Penobscots asserted their right to sovereignty and argued for the authority to set stricter water quality standards on “their” river. But from day to day, out on the water, the two offices work well together, officials said.

By ceding responsibility for monitoring the river to Kusnierz’s office, the DEP can direct its limited staff and funds to other projects, while the Penobscots use federal grants from the Environmental Protection Agency and Bureau of Indian Affairs to cover the river with an intensity the state couldn’t manage. While the DEP uses data from other private researchers, such as lakes associations, the relationship with the Penobscots is unique in its scope.

“We let them do most of the work on the river,” said Dave Courtemanch of the DEP. “The quality of their work is excellent – it’s as good as anything we can do.”

Mitchell and several other researchers have formally studied water quality monitoring at a BIA training program in the Southwest. But nearly all of the reservations’ residents have a stake in the river’s health. Students in the island school raise Atlantic salmon to release into the river, and dozens of tribal members turned out for a workshop on reducing pollution from household runoff, Kusnierz said.”It doesn’t seem to take a whole lot to get people invested in the river … it’s a real honor to be entrusted to look after it,” he said.

“It’s sacred to us.”