It has been a tough year for fish on two of the Bay’s major tributaries, as a mystery illness killed 80 percent of adult smallmouth bass and redbreast sunfish in parts of the Shenandoah River, while ugly skin lesions have turned up on large numbers of smallmouth bass on the Susquehanna River, where some fish kills have also been reported.

Starting in April—while they were spawning and their immune systems were suppressed—smallmouth bass as well as redbreast sunfish on the South Fork and mainstem Shenandoah began developing lesions. Locals described them as cigar burns or canker sores.

Before long, dead fish could be seen floating in the water, ultimately affecting about 80 percent of the two species’ mature populations over more than 100 miles of the two rivers. A similar fish kill occurred last spring on the North Fork of the Shenandoah, and two years before that on the South Branch of the Potomac. Young fish appeared to be unaffected.

“This is not a typical fish kill,” said Steve Reeser, a fish biologist with the Virginia Department of Game and Inland Fisheries. A more typical kill can be traced back to a source of pollution like a chemical spill or a pipe from a sewage treatment plant.

In this case, biologists suggest that low water quality caused by excess nutrients, compounded by other environmental factors, is likely causing the problem. In late July, Virginia officials established the Shenandoah River Fish Kill Task Force to try to determine why fish have been dying on the river.

The situation on the Susquehanna was clearer. The state Fish and Boat Commission said the lesions and fish kills affecting smallmouth bass were caused by a common bacterial agent, Flavorbacterium columnare.

The commission said the fish likely became vulnerable to the infections because they were stressed by unusually warm water temperatures as well as unusually low dissolved-oxygen conditions in parts of the Susquehanna and the Juniata, a major tributary.

The infections were found in fish in many parts of the basin, but were most severe in the Juniata below Lewistown, and in the Susquehanna between Sunbury to just south of Harrisburg.

But biologists were at a loss to explain why the affliction was turning up in the Susquehanna and not other major river basins in the state. “We may never know,” one commission biologist told the Philadelphia Inquirer.

— The Associated Press contributed to this report