COLUMBIA, Pa. -- As trucks thundered across the Route 30 bridge above them, three men in chest waders quietly slipped into the Susquehanna and began jabbing the shoreline water with stunning bolts of electric current.

Momentarily dazed, fingerling fish bubbled up and were quickly netted, measured and scrutinized before being released.

Mike Kaufmann, the chief fisheries biologist in the southeastern area office of the Pennsylvania Fish and Boat Commission, has been doing these summertime surveys of the lower river's juvenile smallmouth bass population since 1986.

Fish are electro-shocked in 300-meter sections along the shore where smallmouth fingerlings hang the first few months of their lives to avoid predators.

The Susquehanna and Juniata rivers were among the East's most prized smallmouth fisheries, and these young-of-the-year classes up and down the rivers were the same: healthy fish and plenty of them. It got so predictable that the surveys were suspended in 2004 and 2005.

But these are very different times on the rivers.

Mysterious fish kills of fingerling bass in 2005 and 2007, and the appearance of round sores like cigarette burns, have alarmed anglers and all who care about the river.

An unprecedented three-year, $378,000, multi-agency probe into what's happening to the fish and water quality has been launched.

Mr. Kaufmann and crew's sampling wades have taken on more earnest meaning.

The day before, the three-man team was buoyed by what it found along a 300-meter stretch of the river near Falmouth: 53 smallmouth fingerlings from this year. It was the highest concentration of young since 1999.

Equally good news was that only one of the fish exhibited any external health problems, a case of tail rot, caused by a fungus infection.

But as the three surveyors made their way along the banks on both sides of the Route 30 bridge, results were troubling.

Twenty-five fish were netted -- not a bad result in terms of numbers -- but eight had ugly white sores and another had tail rot. Moreover, two dead fish were found floating during the sweep and some of the fish that didn't exhibit sores were acting sluggish, suggesting they may be in the early stages of developing problems.

"Some of the fish died in our hands. They are probably diseased," Mr. Kaufmann said.

"It's really hard to tell what's going on. These are fish that have been in the water only weeks."

Similar surveys are being conducted up and down the Susquehanna between the New York and Maryland lines, as well as West Branch, and the Juniata.

It's too early to get a read on this year's population of young smallmouths and their health because survey results up and down the rivers are still coming in, said Bob Lorantas, the Fish and Boat Commission's warm-water unit leader.

"I've received some very good reports and some very so-so reports," he said.

The juvenile class this year will need four to six years to reach legal size of 15 inches.

On the plus side, water conditions were favorable during the spring spawn, there haven't been any sizable fish kills reported and, so far, the river has not slipped into the low levels and warm temperatures when fish are most susceptible to infections from bacteria always present in the water.

The Susquehanna River Water Quality Study, meanwhile, will attempt to determine if there are any pollution culprits out there. Juvenile surveys, such as the one done at Wrightsville, York County, may be helpful in ferreting out any localized problems, Mr. Lorantas said.

Meanwhile, "the river structure now is toward older fish," notes Mr. Kaufmann. Local guides report catching large fish, but the days of catching many are gone, at least for a few years.

Bob Clouser, the famed fly fisher in Middletown, reported catching only five fish in four nights recently while fishing the river's earlier-than-normal white fly hatch. It's a time when anglers used to be able to count on a fishing frenzy.

"The bass just aren't there," Mr. Clouser said disgustedly.