During his 36 years with the Pennsylvania Fish and Boat Commission, John Arway has repeatedly faced off against those he sees threatening the state’s waterways. Once, he said, a coal miner attacked him across a boardroom table. Another time, a gas driller tried to run over him with a backhoe. Through it all, the mild-mannered biologist persevered, using the facts and his agency’s authority under the law to protect the state’s treasured streams and the fish that call them home.

But for the last 11 years, since young smallmouth bass with lesions began appearing in the Susquehanna River, Arway, now the commission’s executive director, has tangled with a more vexing adversary — one that is supposed to be his partner.

Arway has been agitating for the Pennsylvania Department of Environmental Protection to declare the lower Susquehanna River impaired for aquatic life because of the shrinking numbers of young-of-the-year smallmouth populations and the blotchy conditions of their skin. Department officials spanning three administrations and seven secretaries have consistently said they don’t have enough information to do that, despite several of their own reports, as well as those from other agencies, indicating that the river suffers from various pollution problems.

Arway said there’s ample evidence to demonstrate pollution is hurting fish, even if the science has yet to pinpoint precisely how.

“I don’t believe that people should have to adapt to an unhealthy river, especially if we have the tools to fix it,” Arway said. “We have the tools. We just don’t have the will.”

Getting a river listed as impaired under Section 303(d) of the federal Clean Water Act would require the state to identify the cause of the problem and develop a cleanup plan similar to what’s in place now to drive water quality improvement in the Chesapeake Bay. An impairment listing can also help rally community efforts and prompt state and federal agencies to direct funds toward remedies.

Arway argues that the state knows what’s causing the problem with the Susquehanna’s smallmouth bass: phosphorus and herbicides from farm fields and lawns; nitrogen from sewage treatment plants; runoff from stormwater; and endocrine disruptors from disposed personal care products and pharmaceuticals. They are the same pollutants that stress the Chesapeake Bay, which since 2010 has been on a pollution diet known officially as a Total Maximum Daily Load, or TMDL.

The Susquehanna, like the Chesapeake, is fighting two kinds of pollutants — those from nutrients and sediment, and those from synthetic chemicals. Though the Bay’s TMDL calls on the states to reduce the nitrogen, phosphorus and sediment getting into the river, it does not include limits for herbicides and endocrine disruptors.

And while excess phosphorus leads to algae blooms and low-oxygen conditions that stress fish, the DEP’s research has not pointed to the nutrient as the cause of the sick bass.

DEP officials have also acknowledged they’re concerned that they could be challenged in court if they listed the river as impaired for aquatic life without enough data to pinpoint a cause. There is precedent for that worry. The Pennsylvania Farm Bureau led what became a national lawsuit against the Chesapeake Bay TMDL. The Farm Bureau lost when the Supreme Court declined to hear the case, but it cost a lot of time and effort to defend the pollution limits.

“Before we start implementing a solution, we need to know what the problem is, and what the scope of the problem is,” said Patrick McDonnell, acting DEP secretary, during a webinar to promote the release of his agency’s draft Integrated Water Quality Report.

McDonnell praised the Fish and Boat Commission for its advocacy on behalf of bass. But the DEP report classified as impaired just four miles of the nearly 464-mile river, a stretch close to downtown Harrisburg — and then only for recreation — because of high levels of fecal coliform bacteria. The department did list some Susquehanna tributaries as impaired for recreation and aquatic life, but not because of the river’s troubled smallmouth bass, which were once so abundant that Arway and other skilled anglers could catch more than 50 fish in a night.

DEP spokesman Neil Shader added that the Susquehanna was being treated like any other river in the state; the Fish and Boat Commission’s listing request, he said, “would only occur at this point if we were to apply our regulations in a different or unique way.”

Arway was not placated. He panned the DEP verdict in a tweet: “11 yrs of study and still no decision?”

Pennsylvania is unusual in that it places responsibility for overseeing fishing and boating and its game lands with independent commissions. The executive director answers to the commissioners, who are appointed by the governor to four-year terms. That insulates commission directors from the kind of political pressures that prompted John Quigley to step down in May as DEP secretary. Quigley had come under fire from lawmakers after sending an expletive-laden email criticizing the environmental community for not campaigning more aggressively against legislative moves to kill gas-drilling regulations his department had proposed.

Pennsylvania’s state constitution also guarantees that “the people have a right to clean air, pure water and to the preservation of the natural, scenic, historic and esthetic values of the environment.”

Even so, observers say, Arway has been unusually outspoken for a government official — especially one who has served as an expert witness for the DEP in court dozens of times and has a long and close relationship with many DEP employees.

“He’s a brave, honest man, and intelligent and educated. And he knows what he’s talking about, and he’s the only person who has the guts to say it,” said Bob Bachman, the former fisheries director at the Maryland Department of Natural Resources and a former Fish and Boat commissioner.

In his Susquehanna advocacy, Arway has published impassioned columns on the commission website under the banner Straight Talk. He’s written letters to newspaper editors, sparred publicly with top DEP officials and urged the U.S. Environmental Protection Agency to override the state and consider listing the river on its own, which the agency has been reluctant to do.

“Sick fish. Sick river. If one looks at the entire body of evidence that includes sick fish, declining fisheries and less recreational fishing, it leads to the conclusion that DEP should list the Susquehanna River as a high-priority impaired and threatened water,” he wrote in the Harrisburg Patriot-News in 2012. “The listing would start the clock on remedying the water quality problems. We need to act now before the fishery collapses and the time for action is too late.”

Arway’s passion has deep roots. Born near Pittsburgh to a steelworker father and a stay-at-home mother, Arway fell in love with fishing at his uncle’s lakeside cabin in Somerset County. The bluegill and bass fishing was so good then that, when his uncle said he’d pay a nickel apiece for each bluegill he caught, the young Arway brought home 25. His uncle paid, and they had bluegill for dinner for the next several nights, and he never made such an offer again.

Arway majored in biology at the University of Pittsburgh and then worked for Westinghouse before getting his master’s degree at Tennessee Technological University. He came to the Fish and Boat Commission as a seasonal employee in 1980 and worked his way up, focusing much of the time on impairments from acid mine drainage. A father of four and grandfather of six, he lives in Lamar, near State College, and keeps an apartment in Harrisburg, where he stays during the week.

The first signal of problems with the bass in the Susquehanna began in one of its main tributaries, the Juniata River, in the 1990s. Anglers were reporting fewer rock bass, where they could once hook dozens a day. Fish and Boat biologists assumed that anglers were taking too many, and decreased the amount fishermen could keep from 50 to 10. Arway says now he wished the commission would have looked deeper, but at the time, he’s not sure biologists had the tools to detect the compounds ailing the bass.

When the diseased young-of-year smallmouth began showing up in the Susquehanna’s main stem in 2005, it shocked the fishing community. The river was so prized for smallmouth that celebrated fly-fishing guides like Lefty Kreh and Bob Clauser routinely took clients there. Arway, who was by then chief of the commission’s environmental services division, swung into action.

“As an angler, I was mad,” he said. “But as a scientist I knew we had to establish the data to solve the problem.”

So Arway commissioned a $500,000 study by the U.S. Geological Survey to help determine why smallmouth bass were dying and to study the tributaries where the mortality was the worst. After the study showed that oxygen levels were lower in areas where the fish were diseased and less plentiful, Arway worked for years and eventually persuaded Pennsylvania DEP officials to raise their dissolved oxygen standards. The state limit was 4 milligrams per liter and the federal standard was five; that one milligram, Arway said, makes a difference for fish struggling to breathe. A primary cause of low dissolved oxygen is too much phosphorus in the water, which leads to algae blooms.

Raising the dissolved oxygen standard was a start, but Arway said it was not enough. He asked Shawn Garvin, the EPA’s Region 3 administrator, to look at phosphorus fertilizer regulations for Pennsylvania that would be similar to the rules Maryland has adopted. Arway also has suggested a voluntary pollution-reduction plan for the river, which would mirror the mandatory ones for the Chesapeake. And knowing that every two years the state would re-evaluate the rivers and streams eligible for the impairment listing, Arway launched his one-man public-relations campaign to showcase the plight of the smallmouth bass in the Susquehanna.

Though his predecessor bumped heads with the commissioners over what has been described as “philosophical differences” and eventually left, Arway’s board has formally supported his push to declare the Susquehanna impaired and worked with him to keep the issue alive. They support the mission, if not always the tactics.

“John can be a bull in a china closet,” said commissioner Warren Elliott, a longtime Arway supporter and friend. “There have been times that some commissioners thought John ought to be not quite so direct.”

Arway even partnered with a nonprofit to launch Save Our Susquehanna, a go-fund-me campaign of sorts to raise money for restoring the river. (FirstGiving, which focuses on nonprofits, is hosting the campaign.) So far, it has collected $50,000 in small donations from anglers and outfitters, plus $50,000 in commission-matching funds, he said. It’s enough to start work on restoring a small tributary, Limestone Run; but it’s only a fraction of what the state could do, he said, with the resources that would come from a listing.

“It certainly is unusual, particularly for Pennsylvania, to have someone so willing to be so public about his professional and personal opinion,” said Harry Campbell, state executive director for the Chesapeake Bay Foundation, which also is campaigning to have the lower Susquehanna declared impaired for aquatic life. “He is a government official with a scientific background, and that gives him respect among the fishing community.”

Arway was hopeful last year, when the DEP undertook a rigorous scientific study dubbed CADDIS that looked closely at many pollutants in the river. A team of scientists collected more than 30,000 water-quality records and reviewed existing research to isolate the causes. It concluded that the most likely causes of the smallmouth bass’ decline are endocrine-disrupting compounds and herbicides, as well as pathogens and parasites.

But even after that report, DEP officials said there was still not enough information to list the river as impaired.

Others in state government respect his passion on the Susquehanna issue, but say it’s not backed up by science.

Russell Redding, Pennsylvania’s agriculture secretary, bristles at Arway’s assertion that fish are getting sick from phosphorus and herbicides applied to farm fields. Redding said he doesn’t believe designating the river impaired is helpful until the state has nailed down the causes. And while acknowledging that the state’s lagging Bay cleanup effort needs “higher accountability,” the agriculture secretary said he would like proof of what’s hurting bass before imposing limits on farmers’ use of phosphorus to fertilize their crops, as Arway is advocating.

“We all know how complicated this is, and we need the science to guide us, and right now it’s not conclusive,” said Redding, who served under Gov. Ed Rendell, a Democrat, and returned to the job when Democrat Tom Wolf won the office in November 2014. “The problem is still not in context if you haven’t answered the question of why. I prefer to make statements with science on your side.“

Arway is not giving up on the listing, but he’s also turning to other ideas to protect the Susquehanna and its fish. He’s supporting the Pennsylvania Water Resource Act, introduced this year by Rep. Mike Sturla, a Lancaster Democrat, which would charge large industries for water withdrawal and raise $245 million a year for river restoration projects.

Years ago, Arway sued the DEP over permits that he felt did not safeguard water quality from acid-mine drainage. He is not saying that he would take that path over the listing, but he also said he is not ruling anything out at the moment. Whatever the path, he said he wants to make sure he’s not head of the Fish and Boat Commission when an angler takes the last bass out of the Susquehanna.

“If we don’t act soon, we run the risk of delaying our decisions due to our fear of the unknown,” Arway wrote in his column to be posted in September 2016. “So, which fear will determine the fate of our bass? Fear of the known resulting in action, or fear of the unknown and inaction? I will continue to advocate for urgent action. Our bass depend on it, our anglers expect it, and our constitution requires us to do our duty.”