Idaho’s sewer system is the Snake River

As Big Ag flourishes, this massive waterway suffers.

  • Kirk Anderson
  • Irrigation headgate on the Henry's Fork, a tributary of Idaho's Snake River.

    Kirk Anderson
  • A panoramic view of the Snake River from the canyon rim just a few miles upriver from the town of Marsing in southwestern Idaho, where the irrigated plain is surrounded by desert.

    Kirk Anderson
  • The Snake River winds through farmland south of Boise, Idaho.

    Kirk Anderson
  • An aerial view of one of the many industrial dairy farms dominating the landscape of southern Idaho.

    Glenn Oakley
  • Agricultural runoff into the Snake near Homedale.

    Leo A. Geis, Idaho Airships Inc.
  • Boats float beneath a depleted Shoshone Falls. So much water is diverted for hydropower and irrigation above the falls that sometimes it's only a trickle.

    Kirk Anderson

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Point sources are typically sewage plants or factories, the sort of Rust Belt polluters that repeatedly set Ohio's Cuyahoga River on fire back in the 1950s and 1960s, one of the triggers for the passage of the Clean Water Act in 1972. Farm fields – the source of most of the nutrient loading, most of the nitrogen, in the Snake system – are considered "non-point" sources and therefore don't count. Yet wherever nitrogen, phosphorus and other fertilizers leach into streams, they stimulate the growth of algae that deplete the oxygen levels in bodies of water, which can eventually achieve a lethal condition called "anoxia." This process is most evident in the famous Dead Zone, where the Mississippi River empties runoff from the Midwest's Corn Belt into the Gulf of Mexico – a state-sized aquatic zone wholly anoxic and therefore dead, devoid of marine life. No doubt: Nitrogen and phosphorus kill rivers.

We can see more regulatory unfairness in the sewage-treatment plants along the Snake: They're forced to limit their discharges into the river, at taxpayer expense, while the privately operated farm fields are not regulated. And we can see some regulatory gray areas just downstream of Pocatello, where another Snake River tributary, the Portneuf River, flows beside a large Simplot factory that renders phosphate from local mines into mountains of fertilizer each year, while generating polluted wastewater. A billboard in front of the factory proclaims: "Fertilizer: Life's main ingredient." Poets might take issue with that, but it's true enough in a limited sense. The fertilizer factory would appear to be an obvious "point source" of pollution contributing to the Portneuf River's failure to meet the Clean Water Act standards. But the regulators have struggled to get leverage on this cog of the industrial agriculture on the Snake River plain, because the fertilizer factory doesn't directly pipe its phosphate-laden discharge into the river. Instead, the company pumps its wastewater to settling ponds, and from there, for many years it percolated through the soil to the Portneuf River.

The company argued that its riverside fertilizer factory was exempt from 303(d), and EPA regulators decided not to attempt a prolonged legal battle on that disagreement. Eventually, the agency found another lever, through an unrelated Superfund site cleanup it's forcing Simplot to do, and the company has agreed to line the fertlizer-factory ponds to reduce the likelihood of leaks into groundwater and the river system (a likelihood that is never reduced to zero because pond liners also have a habit of leaking). In effect, the regulators' victories come inch by inch, while the impacts of industrial agriculture advance by acres and miles.

What about the feedlots? Legislation subsequent to the Clean Water Act designated feedlots as point-source pollution, so the EPA could regulate them under the act if they discharged into the river or had a potential to do so during floods and storms. But the industry successfully sued to remove that provision, so now the EPA can regulate feedlots only if a factory-like pipe conveys liquid manure to the river. Feedlots are completely free to pump that same manure onto sandy soil fields a stone's throw from the riverbanks, even though the U.S. Geological Survey hydrologists have maps, computer models, well samples and 3-D drawings that show how manure flows to the river through the soil. This is another form of magic: A science agency sees it, but the other agency – the one that regulates – doesn't.

The EPA knows full well the threats posed to water quality by the explosion of feedlots along the river, but under the current legal framework, all it's done is institute a voluntary program of self-inspections and self-regulation. How's that going? "We know we have large CAFO (feedlot) facilities, but they have made the business decision to not participate," says Jim Werntz, EPA's director in Idaho. "Right now we have zero participation in Idaho."

As our springtime journey continues downstream of Twin Falls, we pass a wonderful and melancholy stretch of the river called Thousand Springs, where a great deal of the aquifer's underground flow finally gushes from the canyon walls and joins the river proper. Basically, it's all hard-used irrigation water percolated down from the vastness of chemically dosed fields and feedlots, carrying the nitrogen, phosphorus and other components of the fertilizers, and residues of the manure, pesticides and herbicides. Fish farms – another cog, producing millions of pounds of rainbow trout per year (Idaho leads the nation in cranked-out trout) – use the canyon springs to grow their product, a process that generates additional phosphorus and nitrogen discharges into the river, in the form of fish feces, among other things.

Farther down the river, still more cattle feedlots cluster around Marsing, southwest of Boise. These feedlots have discharged manure by spreading it as a liquid three inches thick and miles wide on surrounding farm fields, which are crusted over with dried muck. The feedlots weren't here 10 years ago, and now they confine about 15,000 Holsteins within a half-mile of the river. And so forth.

Just as Idaho's Snake River ag factory has a beginning, it has an end. Where the river approaches the Washington border, there are three final reservoirs directly receiving runoff from the Snake River Plain: Brownlee, Oxbow and Hells Canyon. (The four dams and reservoirs down on the Washington stretch of the Snake River, also built to benefit farmers, are not so directly related to the Snake River Plain.) Here, then, is where we do our final accounting.

We can do this accounting quantitatively, if you like, using numbers for sediment and nutrients sampled in the Brownlee, Oxbow and Hells Canyon reservoirs that exceed EPA standards. Definite readings of rampant algal blooms, anoxia and fish kills. There are even advisories issued by the state government, warning people not eat reservoir fish owing to mercury contamination of the tissue. It's difficult to determine the mercury's source exactly, but industrial ag has an important role. Mercury occurs naturally in soils and gets released into the atmosphere by operations such as crushing limestone to make cement, but that form of the element doesn't bioaccumulate in fish and humans. First, it must be chemically transformed in a process called methylation, which is made possible by the chemical composition of the nutrient-laden sediments of the reservoirs.

In another unusually frank conversation, some USGS hydrologists in Boise discuss the problem. One of them, Greg Clark, is especially blunt. "Every year you get this layer on the bottom (of Brownlee Reservoir) that goes anoxic, and then you get perfect conditions for creating methyl mercury."

Clark corrects the impression that the range of pollutants from industrial ag goes completely untreated. He sees the entire Snake as a sewage system, with the reservoirs at the bottom end acting as de facto sewage-treatment lagoons. Clark explains it using the terminology of that science: The three huge reservoirs/lagoons provide primary, secondary and tertiary treatment. He actually uses those terms.

"We should show the videos of what the bottom of Brownlee looks like," he says. "It looks like a sewage-treatment facility. Fine-grained muck. It's really nasty stuff. It looks like the bottom of a septic tank. We took a rover and went down and took videos, and there's all these little organisms down there decomposing stuff and there is gas bubbling up. It's nasty. It's nasty."

So this is the end, for now. One could argue with a mix of cynicism and dark comedy that this sort of sewage treatment works by sending relatively nutrient-free water downstream to the Columbia, where farmers can repeat the process of fouling it. But even the darkest comedians have no experience with reservoir-sized treatment lagoons hooked to a state-scale sewer. The reservoirs are filling day by day with toxic, mercury-laden sludge in layers to match the mountains. What will happen when – eventually and inevitably – almost 30 square miles of reservoirs fill with enough sludge to cover 2,700 square miles of land a foot deep? No one knows the answer. This problem we leave to future generations, as is our habit.


A few corrections and clarifications: The editing process introduced two mistakes in the version printed in the HCN magazine; both have been corrected in this online version. First, the dams in the Hells Canyon of the Snake River are not easier on salmon than downriver dams; in fact, they allow no fish passage, so those five words have been deleted from this online version. Second, the Chobani yogurt factory in Twin Falls is roughly a million square feet, not 100 million square feet (a mistake by the Idaho Dairymen's Association, which we repeated). And clarifying what we reported about the ingredients of Chobani yogurt: Chobani says its yogurt is natural, because the thickener, colors and flavors are derived from plants; that's an argument, because healthy-food advocates think those additives are artificial, and the federal government has not imposed a legal definition of "natural."


Richard Manning, based in Helena, Montana, has authored nine books including Go Wild, published earlier this year by Little, Brown and Company, and his freelance writing has appeared in a range of national publications including Harper’s and The New York Times.

This story was made possible with support from the Kenney Brothers Foundation.