Pennsylvania Department of Environmental Protection Secretary Michael Krancer has rejected a request from the Pennsylvania Fish and Boat Commission to list the Susquehanna River as impaired after the discovery of a large number of smallmouth bass with black lesions on them.

In an April letter to Fish and Boat Commission Executive Director John Arway, Krancer said he shared the concerns about the Susquehanna. But listing the river wouldn’t solve the problems, he said, because no one had yet identified the pollutant that was causing the lesions.

The lesions have been showing up in smallmouth bass along a 98-mile stretch from the Holtwood Dam to Williamsport for three decades, but anglers report that they are seeing it more in recent years. While the fish, called “blotchy bass” or “black spot bass,” are safe to eat and handle, the number of infected fish was alarming enough for Arway to make his request.

Arway’s letter follows an appeal in August 2011 from multiple organizations including PennFuture, Trout Unlimited, the Chesapeake Bay Foundation and American Rivers (which had once designated the Susquehanna as the nation’s most endangered river), to list the river and further study the problem.

Arway has also taken his cause to the public through speeches and op-eds.

“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. “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.”

The lesions are not the first problem to emerge for fish in the Susquehanna. In 2005, there was a high mortality with young-of-the-year smallmouth bass. Efforts to stock and restore shad have not been successful. And scientists have found high incidences of egg precursor cells in the Susquehanna’s male smallmouth bass, a sign that some sort of pollution is affecting the water quality.

Brian Mangan, director of the environmental program for King’s College as well as a biology and environmental science professor at the Wilkes-Barre school, said the decision to list a river is best left to politicians. But, he said, it’s clear scientists need more data to determine what’s happening to the Susquehanna’s smallmouth bass. In addition to lesions and intersex fish, Mangan and his colleagues have discovered outbreaks of columnaris bacteria under low-oxygen conditions. These fish have a dark circle or an oval on them.

While some residents have suggested that natural gas drilling is to blame, Mangan said that’s the one thing he’s sure isn’t causing the problem. Instead, he said, the problem may stem from a warming trend in the water, or the invasion of the ravenous rusty crayfish, which is taking away habitat.

“There are environmental stressors that we do have to face down. Labeling the Susquehanna as impaired may be one of the ways we get attention to the river, and do more research,” he said. “We’ve got to find out more information about what’s going on before we know what has to be done.”