The South Branch of the Potomac River is as clear as bottled water here, where it rolls over a bed of smooth stones about 230 miles upstream from Washington. But there is a mystery beneath this glassy surface.

Many of the river's male bass are producing eggs.

Scientists believe this inversion of nature is being caused by pollution in the water. But they say the exact culprit is still unknown: It might be chicken estrogen left over in poultry manure, or perhaps human hormones dumped in the river with processed sewage. Chances are, it is not something that federal and state inspectors regularly test for in local waters.

The discovery has made the South Branch the latest example of an emerging national problem: Hormones, drugs and other man-made pollutants appear to be interfering with the chemical signals that make fish grow and reproduce.

While researchers look for answers in West Virginia, other scientists are testing Rock Creek, and another group is seeking financial support to test the rest of the Potomac to see whether they can find the same troubling effects downstream.

"Whatever's doing this to the fish may be the canary in the mineshaft," said Margaret Janes, a West Virginia activist with the Appalachian Center for the Economy and the Environment.

Scientists say it's still too early to tell what these findings will mean for the bass population in the South Branch; they aren't sure whether the affected males are still able to reproduce. And no one is aware of any effects on human health in the Potomac watershed.

But scientists believe that fish might be the first to absorb any dangerous chemicals that might later affect humans.

"They're likely to be hit first," said Mike Focazio, a researcher with the U.S. Geological Survey. "We look there, and it seems to be happening."

The situation in West Virginia was discovered by accident, when scientists from the state and the geological survey were called in to investigate reports that fish in the South Branch were developing lesions and dying en masse.

They dissected dozens of bass caught last summer, mainly smallmouth bass. They found no obvious cause for the lesions or deaths, but did discover that 42 percent of the male bass had developed eggs inside their sex organs.

The study surprised scientists. Though the South Branch has been cited for problems with bacteria from poultry manure, state officials said it did well on most aspects of water-quality testing.

"We always have, and still do, look at this as one of our highest-quality fisheries," said Patrick Campbell of the state Department of Environmental Protection. "It's counter-intuitive to think we would have this type of problem out there."

But the problem is there: A follow-up survey in the spring found even higher rates of "intersex" bass -- as the affected males are called. A study of 66 male smallmouths from the South Branch found that about 79 percent showed such symptoms, according to U.S. Geological Survey data.

The scientists are now analyzing water samples from the South Branch and the Cacapon River -- a nearby Potomac tributary where intersex bass were also found. The chemicals they're looking for now are not the well-known pollutants that the state already tests for, such as nitrogen and phosphorus from manure and metals from mine runoff.

Instead, the culprit is probably in a class called "emerging contaminants," which includes everything from caffeine and prescription drugs to hormones excreted by livestock or humans.

Some of these pollutants have been linked to developmental problems in wildlife. Scientists believe that fish, especially, absorb hormones from other animals, as well as other chemicals that their bodies mistake for hormones.

One recent study near sewage plants in Colorado found male fish whose bodies were trying to produce eggs and some females whose reproductive systems were out of sync. Other studies have found similar effects from the hormones in cow manure and from chemicals from a wood-pulp plant.

"It is certainly an alarming situation that we're seeing more and more gross effects," said David O. Norris, a professor who worked on the Colorado study.

These emerging contaminants were hard to detect without the finely tuned equipment developed recently. The first nationwide survey, conducted in 1999 and 2000, found hormones in about 37 percent of the streams surveyed and caffeine in more than half.

The only testing in the Potomac, done in Washington in 2002, found low levels of caffeine, plus the insecticide DEET and chemicals produced when a body breaks down nicotine. There were also a few suspected endocrine disruptors, including chemicals found in hand soap and household cleaners.

As of now, little is done to test for these chemicals -- either in river water or in drinking water. The U.S. Environmental Protection Agency has not set standards, saying more research is needed to determine which contaminants are harmful and what levels are unsafe.

West Virginia, Virginia, Maryland and the District do not test river water regularly for drugs or hormones. The same goes for drinking water after it is processed by the Washington Aqueduct, supplying the District, Arlington County and Falls Church, and the Washington Suburban Sanitary Commission.

Still, the West Virginia study has spurred scientists to look for more information. Researchers at the U.S. Fish and Wildlife Service are seeking money for a much larger study across the Potomac watershed. They want to look for intersex bass and potentially disruptive chemicals in sites including the Blue Plains sewage plant in Southwest Washington.

Another federal study is underway in Rock Creek, looking for intersex symptoms and other health problems in a species of fish called white suckers.

Scientists across the region stressed that their work is just beginning. "We really don't know what's going on," said Vicki S. Blazer, a researcher for the geological survey in West Virginia.

The Potomac's South Branch in Moorefield, W.Va. The bass problem was found after reports of many fish dying with lesions.Activist Margaret Janes said, "Whatever's doing this to the fish may be the canary in the mineshaft."