By Shannon McGovern
In April of 2003, Virginia’s Environmental Quality Department received a call from a resident living on the North Fork of the Shenandoah River that initiated an investigation into the mysterious deaths of large populations of fish. The following spring, dead fish bobbed to the surface along 100 miles of the South Fork. By 2005, about 65 percent of the fish population

had died, 13 times the number of fish deaths that is typical to any normal year.
Almost a decade later, state officials do not fully understand the causes of the two-year-long “fish kill,” but they have identified a bacteria common to the affected rivers. And while fish mortality rates have dropped since 2005, the bacteria, a strain called Aeromonas salmonicida, is still present in the Shenandoah and nearby waters.
Aeromonas salmonicida typically thrives in coldwater environments where the temperature stays below 65 degrees year-round. Its appearance in the Shenandoah was a mystery for Paul Bugas,
aquatic manager for the Virginia Game and Inland Fisheries Department.
“It really surprised us to find bacteria in the Shenandoah, which is a warm body of water,” Bugas said.
A seasonal problem
Bugas said the bacteria infect large schools of fish, causing tissue damage known as “lesions.” Lesions cause afflictions ranging from minor, superficial sores to penetrating, fatal tissue damage that can cut as deep as a fish’s backbone.
Typically affected fish are eight inches or longer. Popular game fish such as the redbreast sunfish, rock bass and smallmouth bass have all been found with bacteria-induced lesions.

“The Shenandoah is probably the most popular fishing river in Virginia,” said Jay Gilliam, an official with the Virginia Association of Soil and Water Conservation Districts. “And bass is the fish they are looking for.”
Fish are particularly susceptible to pathogens and parasites in the spring, when their metabolism picks up because of increased feeding and spawning. Since 2003, fish deaths have been observed for about two months, beginning in April and ending by Memorial Day. When the waters warm again, the bacteria subside.
The Shenandoah River, which has been the most severely affected Virginia river, forms just north of Fort Royal, Va., where the South Fork Shenandoah River meets the North Fork Shenandoah River. The Shenandoah then flows north to Harpers Ferry, W. Va., where it joins the Potomac River.
History of pollution incidents
Because the Shenandoah covers several districts, fish kill research has been a multi-agency effort involving the U.S. Fish and Wildlife Service, the Virginia Environmental Quality Department and the Virginia Game and Inland Fisheries Department, as well as citizens’ groups and local advocates.
The Shenandoah has a history of pollution incidents. According to the Environmental Quality Department, between 1929 and 1950, mercury waste from a now-defunct DuPont Co. facility contaminated the South Fork from Waynesboro to Front Royal.
While the mercury has mostly settled and does not appear to pose a significant health threat, its concentrations have not declined. A mercury advisory on the Shenandoah has remained in place, and DuPont continues to sponsor a program led by scientists who monitor fish health and water quality.
Between 2003 and 2006, scientists observed what Bugas calls “the heyday of the fish kills.” Then in 2007, scientists discovered the same phenomenon happening in James River—a totally different watershed.
“That’s just purely weird because there’s no connection between them,” said Gilliam. “It’s been a complete mystery.”
‘Perfect storm’ of factors
More recently, scientists have not seen fish mortalities like those they saw back in the early 2000s. In the past few years, only 5 to 10 percent of fish seem to be affected by Aeromonas salmonicida, but Bugas said that does not necessarily mean large-scale fish kills are a thing of the past.
“I don’t want to say this thing has played itself out because we still see fish health issues in the Shenandoah and the James,” said Bugas. “But we don’t have the fish kills where thousands of fish were belly up.”
Bugas says scientists still do not know precisely what caused the widespread fish kills almost a decade ago. He acknowledges that it could have been the result of a single environmental trigger, but says it is more likely that a variety of factors contributed to the problem.
“I think this bacterial infection back in 2003 and 2004 was a perfect storm of environmental circumstances where the fish were susceptible,” he said.
Bugas also noted that today’s watersheds are under stress from a variety of human uses and influences, from water supply demands, waste disposal and irrigation, to hydropower, transportation and recreation. Rivers are also receptacles for materials that run off the land, including agricultural, household and industrial waste.
“We ask a lot of our river systems as a society,” said Bugas.
A problem of stress
Scientists have pointed to pharmaceuticals and hormones from sewage treatment facilities as contributing factors to the fish deaths. Bugas said there are many endocrine disruptors found in household products, such as certain soaps, that seem to affect fish immune systems. They have also found more dramatic phenomena, such as eggs in testes of male fish.
Scientists have not identified a direct correlation between endocrine disruptors and the fish kills, but they do believe pharmaceuticals, pesticides and parasites have brought added stress to fish immune systems, affecting their ability to fight off bacterial infections.
“Stress is what kills you,” said Gilliam. “The source of stress might come from anywhere. With fish, if they get into a place where there’s not enough dissolved oxygen, where the water is too warm, where there’s not enough food… these are all sources of stress.”
Scientists continue to monitor fish populations in the Shenandoah every spring, keeping an eye primarily on fish health, but also to ensure the water and fish pose no significant hazard to anglers or people using the river for recreation.
Bass populations have grown since 2004, but Bugas noted that repeated fish kills could keep visitors away from the Shenandoah River, causing a loss of tourism, fishing and other water sport-related revenues.
“It’s still in the back of our minds and we just don’t have the staff or money to dedicate to research,” said Bugas. “So we are just monitoring in the springtime and keeping our fingers crossed that this thing doesn’t emerge as a huge killer in the future.”