Eight years ago, it appeared something was wrong with the smallmouth bass in the Susquehanna River.

Thousands of young fish were dying in the heat of July and August, many showing lesions on their shimmery skin. In favorite fishing holes, where anglers could once catch close to 100 fish a day, they were finding few fish alive.

It alarmed John Arway, an aquatic biologist who has spent more than 30 years with the Pennsylvania Fish and Boat Commission, the independent state agency tasked with protecting aquatic resources and promoting fish and boating opportunities. As the agency continued to monitor the situation, conditions worsened. Smallmouth were discovered with lesions as well as with black blotches on their skin, and many male fish had the beginnings of female eggs in their testes.

Recreational fishing in Pennsylvania is a $3.4 billion industry, and the Susquehanna River has long been at the heart of it. As anglers continued to report sick fish and poor catches, commission biologists were documenting cases of algae blooms, areas of low-dissolved oxygen and increased pH levels.

In 2010, when Arway became the commission's executive director, he began pushing the state and the EPA to list the river as "impaired," a designation that would make its cleanup a priority. Impaired rivers, which are on what is known as the 303d list, could potentially receive more federal and state dollars for cleanup. They also trigger a total maximum daily load designation, which puts in place a stronger framework for reducing pollution and sets a timetable to clean up the river with penalties if the entities don't follow the schedule.

Environmental advocates, anglers and conservation groups, in letters to the commonwealth and the EPA, also requested that the river be listed as impaired, but to no avail.

The Pennsylvania Department of Environmental Protection pushed back, saying it didn't know what was causing the problems, and therefore couldn't list the river as impaired.

And in May, the EPA agreed with the DEP, saying there was not enough information to list the river as impaired.

Arway is not against further study to determine causes. But, he said, the river needs to be on the impaired list now, regardless of the reasons, so its cleanup becomes a priority.

"Until we get it on there, we're not recognizing that the river is in trouble," Arway said. "The listing gives us a timetable to fix it."

DEP officials disagree.

"Right now, we still have a lot of data we have to collect and analyze," said Lee McDonnell, the DEP's director for point and non-point source pollution. "We don't feel we have enough information to make a good decision on that. We haven't determined a riverwide impairment at this point."

Several DEP officials attended a May 8 forum at the Midtown Scholars Bookstore in Harrisburg to present their data to a skeptical group of about 50 scientists, anglers and concerned citizens. The forum, which the Chesapeake Bay Foundation organized, is one of several the foundation is planning to draw attention to the smallmouth bass' plight. The foundation has also produced a report, Angling for Healthier Rivers, that outlines the problems and solutions for the Susquehanna.

Josh Lookenbill, a DEP biologist, presented monitoring completed by the agency in 2012 that looked at algae blooms, water chemistry, insects and androgenicity/estrogenicity — a scientific way of saying intersex fish. The research found that the dissolved oxygen levels did not violate state criteria at any of the river sites.

But the agency is largely sampling in the mainstem of the Susquehanna, and the bass spawn and the young-of-the-year live in the shallow areas near tributaries. The agency is also using a standard of 4 parts oxygen per million parts water as its threshold for low dissolved oxygen, or hypoxic conditions. The federal standard is 5 ppm. According to DEP data, many more areas would be impaired under the 5 ppm standard. Arway and his agency have been pushing to change the standard to 5 ppm.

The DEP is also focusing its monitoring and analysis on the benthic organisms — small worms and insects that the smallmouth bass eat. They typically can tolerate pollution much better than fish.

"Anybody that has any sense of science knows that the benthics aren't the whole story," Arway said. "You have to look higher up in the food chain."

He added: "We believe the right indicator for the river is fish. And we know the fish are diseased."

When asked if sampling in the mainstem adequately captures problems in the shallow spawning area, Lookenbill replied that testing in tributaries and extrapolating that information to the river would cause the agency legal problems.

"We'd be taken to court," he said, "And we would lose."

Rod Kime, head of the DEP water quality division, echoed that when he reminded the audience: "We are a regulatory agency. We can be legally challenged…We need good science before we go back to stakeholders and say, 'this is what you have to fix.'"

Some of those fixes would surely be unpopular. Communities in Pennsylvania have already balked at the cost of upgrading sewage treatment plants, which contribute nitrogen and phosphorus to rivers. Farmers have complained about tighter manure management rules that limit when and how farmers can spread and store manure. Maryland residents are railing against a stormwater fee; Pennsylvanians aren't likely to be any happier than their southern neighbors about spending more money every year to keep sediment out of streams.

Rod Bates, a fishing guide with Koinonia Guide Service in Carlisle, PA, said the state shouldn't worry about the fallout, but should instead act swiftly to protect the river he's fished his whole life.

"I quite honestly am disappointed with the DEP," Bates said. "We're doing nothing. How many more years of study? How long do we wait until we do something?"

Vicki Blazer, a fisheries biologist for the U.S. Geological Survey in West Virginia, said she doubts more research will be able to pinpoint one source. Blazer has also studied intersex fish in the Potomac and Shenandoah rivers. She says the Susquehanna smallmouth are dying because of a "perfect storm" of chemicals entering the river: nitrogen and phosphorus from farms and sewage treatment plants, endocrine-disrupting chemicals from hormones in waste and pesticides, and warmer temperatures that provide algae more time to thrive. When the fish become weak, they become vulnerable to parasites in the river.

"These fish are immune-suppressed," Blazer said. "They're getting impaired by whatever's in the water. To me, that means an impaired ecosystem."

Arway is glad that Blazer and other researchers are on the case, but he said the river doesn't have time to wait until they figure out the causes. Last year, his agency closed the bass fishing during the May 1 to June 14 spawning season. At the urging of anglers concerned about reproduction, bass fishing on the Susquehanna is now catch and release.

"My contention is, we have got to start helping this river," Arway said.

"I don't want to be the director in the position I'm in when the last bass is caught out of the Susquehanna."

The Chesapeake Bay Foundation report, Angling for Healthier Rivers, is available at www.cbf.org/2013-smallmouth-bass-report-embedded-pdf.