Smallmouth bass, oval shaped and olive colored, are an immensely popular game fish that draws more than 100,000 anglers each year to the Susquehanna River, officials say, and anchor a statewide sportfishing industry with annual revenues of $3.4 billion. Scientists say bass are also a sensitive species whose health reflects the general state of a watershed as a whole. In the last decade, the number of smallmouth bass in the Susquehanna has dropped by roughly 40 percent. In July 2005, thousands of sick, dead fish clogged the river , most of them young smallmouth bass with lesions on their skin, and the outbreaks continue.

“We do think some of the same feminization chemicals are causing immunosuppression,” said Vicki Blazer, a fish biologist for the USGS who helped write the report. “And that disease is having an effect on the population.”

Most troubling, biologists say, is that many of these bass, and scores of others, have visible signs of disease — black splotches on their skin and grotesque open sores.

In Pennsylvania’s Susquehanna River, one of the longest in the northeast, male smallmouth bass are sprouting female egg cells in their testes . According to a United States Geological Survey report released in June , these intersex fish appear in water — both in this river and two others in the state — that has become saturated with estrogenic compounds, natural and artificial hormones in animal manure and, to a smaller degree, sewage.

‘We’ve been trying to explain that the river is sick. And the problem is not because of what we’re doing for the water. It’s because of what we’re doing for the land.’

Late last month, John A. Arway, executive director of the Pennsylvania Fish and Boat Commission, wrote to the Environmental Protection Agency and pleaded for its help in regulating agriculture.

“We’ve been trying to explain that the river is sick,” he said in an interview. “And the problem is not because of what we’re doing for the water. It’s because of what we’re doing for the land.”

The report says there is a significant correlation between the percentage of land used for agriculture in a watershed and the number of intersex fish downstream in a river. The Susquehanna River, a broad waterway with two branches that course through dairy farms and past factories before joining to form the largest tributary to the Chesapeake Bay, has a basin that covers nearly half the state. It is home to 3 million people, and one-fifth to one-half of its land is used for agriculture. The Delaware River, with a smaller percentage of its basin used for agriculture, has fewer intersex fish. There are fewer still in the Ohio River, which has the fewest number of acres devoted to agriculture in its basin, the report says. In the Susquehanna and Delaware rivers, biologists also found white sucker fish with stem cells in their blood that could potentially turn into egg cells, but these and other fish were otherwise healthy.

Estrogen is present naturally in the waste of all animals, particularly females producing milk or eggs. In parts of Pennsylvania, there are now more domestic animals than ever on the land, and manure from them is routinely spread on cropland for use as fertilizer. It washes into rivers when it rains, biologists say.

Between 2002 and 2012, the acres of land fertilized with animal manure grew by nearly 10,000, while the head count of cows rose by almost 30,000 and the number of chickens shot up by more than 13 million. This is according to analysis of data from the U.S. Department of Agriculture’s census of agriculture for the 30 Pennsylvania counties that compose most of the Susquehanna River basin.