Degraded Water Quality

A lack of comprehensive water quality data on the Snake River and its tributaries has long been an issue. Idaho is one of five states not authorized by the EPA to administer the NPDES permit system under the Clean Water Act. As a result of federal permitting backlogs, many NPDES permits have expired. An Idaho DEQ study in 2008, 36% of Idaho streams required TMDLs for failing to meet water quality standards. IDEQ’s last survey in 2008 found that Idaho had 1,392 impaired waters with 2,243 causes, the most common of which are temperature, sediment, nutrients, and pathogens. Despite these designations, implementation and enforcement has been spotty at best, allegedly due to funding issues and Idaho’s lack of NPDES primacy. Idaho and the EPA have a legal responsibility to ensure that impaired waters are dealt with in a timely manner, and SRW aims to ensure that these legal obligations are met.

Dams and Diversions

The Snake River is one of the world’s largest hydropower systems. In addition to the lower Snake River dams which prevent salmon and steelhead migration, there are 11 other major dams upstream of the Salmon River’s mouth in addition to the hundreds of dams and innumerable diversions to tributary rivers and streams that feed the Snake. Many of these dams and diversions are outdated, no longer compliant with legal requirements, and do not produce hydropower. Dams significantly alter the river’s flow, water quality, and fish migration. Logging, water diversions for agriculture, and human population growth have also altered the Snake’s flow regime and water quality, reducing the quality of fish habitat basin-wide. The Snake River’s water quality, and the health of fish, animals, and people that rely on the Snake as a water supply, is also degraded by industrial and municipal pollution, toxic waste dumps, and pesticide and fertilizer runoff.

A Non-exhaustive Key to Major Dams in the Columbia River System



In 2012, Idaho ranked 3rd in the nation for milk production – with 578,000 dairy cows producing 13.3 billion pound of milk and cash receipts totaling $2.43 billion. Idaho’s dairy operations are concentrated along the Snake River and employ industrialized methods of production, processing, and international distribution that bear no resemblance to traditional agriculture. The industrial model requires that true costs of dairy production be externalized in the form of water pollution and depletion, low wages, and decreased quality of life for neighbors.

Dairy is produced in Concentrated Animal Feeding Operations (CAFOs) that house thousands of cows in a confined area. Nearly all of Idaho’s dairy CAFOs drain to the Snake River and its aquifer, and they are estimated to produce more than 12 million tons of animal manure each year. This massive amount of waste is typically stored in open-air pits and then disposed of without waste treatment onto adjacent land as part of the standard industry practice known as “winter spreading”. Inadequately regulated and poorly designed CAFOs – as well as the intensive crop production needed for animal feed – pose serious problems for human health and water quality from nitrates, ammonia, phosphate, pathogens like E. Coli and Salmonella, pesticides, herbicides, antibiotics, heavy metals, and other pollutants.

Because the Snake River and the Snake River Plain Aquifer are hydrologically connected, pollution and depletion of one water resource inevitably affects the other. Major segments of the Snake River are highly polluted by bacteria and nutrients that cause excessive nuisance algae production and low dissolved oxygen levels. Nitrate pollution in the Snake River Aquifer, which is the sole source of drinking water for one-fifth of all Idahoans, affect most of the aquifer and is growing largely due to fertilizer application and dairy facilities. Consumption of water polluted by nitrate is dangerous, especially for young children, and USGS studies show that within 30 years large portions of the aquifer will be undrinkable.


ish farming in the Columbia and Snake River Basins has been utilized since the late 1800s to provide salmon, steelhead and trout to compensate for fish harvest losses caused by human activities such as the destruction of fish habitat and construction of dams. Hatcheries pollute rivers with their effluent, compete with and displace native fish, and dilute genetic diversity in native populations. Taxpayers compensate dearly for this expensive practice, which compromises coldwater systems by degrading habitat and altering the natural behavioral order while producing only low-quality angling experiences. Studies show that within three months of planting, 95% of stocked river trout are dead – with 80% mortality resulting from non-human predators. Montana stopped stocking trout in streams and rivers containing wild native stocks in 1974, and it now enjoys the country’s healthiest and most productive trout fisheries. Its time for Idaho to regain accountability of tax dollars and recreational opportunities by discontinuing its stocking program. The current practice of stocking rainbows in native cutthroat fisheries is a slow but sure ecological disaster that will result in native cutthroat species are hybridized out of existence, crowded out, and outcompeted unless a paradigm shift in state policy is realized.

Groundwater Contamination

More than 95% of Idaho’s drinking water comes from groundwater. Human activities in the Snake River Basin contribute the major sources of ground water contamination, especially in urban areas. A non-exhaustive list of sources includes:

  • Petroleum spills and leaking underground storage tanks. About 3,500 underground storage tanks are registered in Idaho alone. A pinhole leak from one tank can spill hundreds of gallons of fuel each year.
  • Injection wells and stormwater runoff contaminate groundwater. Oil field injection wells are on the rise in Idaho, and thousands of shallow injection wells already exist.
  • Improperly designed sewage disposal and septic systems, which can contaminate ground water with coliform and other bacteria, viruses, and nutrients.
  • Contaminants from solid waste landfills, hazardous waste storage and disposal sites. Substances that leach and pollute groundwater include metals, solvents, refrigerants, and petroleum derivatives.
  • Sludges from petroleum refining, creosote and solvents from wood treatment, and pesticides from agricultural and domestic insect control.
  • Contamination at hard rock mining operations. Fluids from tailings, cyanide heap leach facilities and leaks may contain cyanide, heavy metals, inorganic chemicals and acidic water.
  • Agricultural practices resulting in saline seep, erosion, sediment and nutrient-rich runoff.

Pollution Increasing In Idaho’s Snake River Aquifer (from Boise State Public Radio)