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Home > Feature Articles > Agriculture & Organic Production

Groundwater Studies Measure Aquifers Contaminants Under San Joaquin Dairies

Agricultural runoff tests track pollutants for regional water tables that supply fresh water for the community

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Dairy cows and water pollution Spring marks the end of the San Joaquin Valley's cold, foggy weather when dairy managers closely monitor their on-farm lagoons to make sure the water flushed from corrals and milking lanes doesn't cause a contaminated overflow.

If rain and runoff push the water surface too close to the brim during the winter, dairy operators have no choice but to pump wastewater onto fields covered with slow-growing wheat, rye or oats that need little nourishment until February, when the region's early spring fuels earnest plant growth.

Growing plants draw up nutrients that otherwise might slip through the soil far below the root zone, where they can contaminate an underground aquifer vital to valley agriculture and people.

The winter season, combined with limited wastewater storage capacity on dairies, is one reason operators can't quite close the dairy nutrient cycle. In theory, the system is nearly seamless: cattle manure fertilizes field crops that become cattle feed.

However, University of California monitoring has confirmed that aquifers below dairy farms are often contaminated with nitrate that makes the water unfit for human consumption.

For the past 10 years, UC Davis Cooperative Extension groundwater hydrologist Thomas Harter has worked with colleagues and dairy operators to create a network of monitoring wells on dairies in Stanislaus and Merced counties, where the soil is sandy and the groundwater in some places is only 10 feet below the surface.

"We found high levels of nitrate in the top 10 to 20 feet of groundwater," Harter said.

Severe contamination not expected in Southern San Joaquin Valley

Many thought the problem wouldn't be as severe in the Southern San Joaquin Valley, where groundwater is deeper and soil less permeable. Monitoring wells were installed in recent years at dairies in Kings and Tulare counties at the behest of the Central Valley Regional Water Quality Control Board.

"Looking at that data, what we see is that, with the exception of a few dairies, there are elevated levels of nitrate on most monitored dairies in Tulare and Kings counties, but it's not nearly as high as we observe in Stanislaus and Merced counties," Harter said.

Even though the wells revealed contamination, the data wasn't able to show whether the contamination comes from the dairies, from nearby orchards or from home septic systems. Scientists don't yet know when the contamination occurs and, if the dairy is found to be wholly or partly responsible, what parts of the operation cause water contamination.

To answer these questions, Harter is coordinating a study on dairies in Kings and Tulare counties funded with a $1.56 million grant from the State Water Resources Control Board and the CALFED Bay-Delta Program. Last summer and fall, rigs drilled wells 140 feet, or about 14 stories, deep next to dairy waste lagoons, near the fields where manure is used as fertilizer, and adjacent to the corrals where cows spend the bulk of their time.

Soil cores reveal the valley's geologic history

The drilling was performed with special equipment that pulled out intact cores of soil. The cores were placed in successive cardboard channels, revealing some of the area's recent geologic history.

"We found layers of fine, gray and reddish sand, packed clay, coarse gray sand layers, very few pebbly areas and much loamy soil," Harter said. "Each part represents a different epoch as the valley floor was laid down, layer upon layer, by muddy floods and in often rapidly changing stream beds, where material was deposited that had been eroding from the surrounding mountains."

The soil cores will help scientists understand the interaction of nitrogen's three forms with the different types of soil. Dairy manure water contains two forms: organic nitrogen and ammonium. When it is exposed to microbial action in soil, the organic nitrogen transforms to ammonium. Over time, the ammonium nitrogen converts to nitrate with the help of the oxygen in the top soil layer. The nitrate is the form that moves easily with water through the soil profile. The casings of the new monitoring wells are perforated at different levels so samples of first-encountered groundwater will be accurately tested no matter the season.

"The groundwater level may vary in any one location by 20 or 30 feet between seasons or over a couple of years depending on rainfall totals," Harter said. "Once recharge water hits the water table, in addition to going down, it will flow laterally along the slope of the water table, so it is important for us to know where exactly contaminated water is found."

'Fingerprinting' technology to pinpoint sources of water contamination

The scientist also plans to study water samples from the wells with fingerprinting techniques to determine what generated any contamination.

"We believe there are many non-dairy sources of nitrate in groundwater," Harter said. "Golf courses, water treatment plants, septic tanks and agricultural operations have all been implicated in groundwater contamination. If we find contamination, we want to know where it came from. We are developing the technology to distinguish between, for example, nitrate derived from synthetic fertilizer and nitrate derived from humans or animals."

Harter said he is confident that the data generated by this project will allow scientists to establish guidelines for monitoring and managing groundwater impact from dairies.

"It's a matter of getting the production management practices down to the right level," he said. "There are issues with the environment in running a dairy. I think we can use the data from this research to help determine how management practices must be modified so dairying can continue in a sustainable and economically viable manner."

A three-minute video in which UC Davis Cooperative Extension groundwater hydrologist Thomas Harter explains the dairy nutrient cycle is available for viewing online at

CONTACT: Jeannette Warnert, (559) 241-7514,

PROBLEM: Intensive farming creates production management practices that concentrates pollutants with resulting water table infiltration. SOLUTION: Sustainable farming practices such as "permaculture" and multi-culture farming practices vs. mono-culture strategies.

Edited by Carolyn Allen, owner/editor of California Green Solutions
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