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Farming, nitrates and the groundwater

By Jessica Fargen Walsh

YORK — It’s a windy November day, the smell of ammonia is strong and Ron Makovicka is doing what he does in the fall — fertilizing hundreds of acres of soybean and corn fields. 


His tractor pokes along at 4 mph with a tank attached to the back that injects anhydrous ammonia into the ground every 30 inches. 


Under new regulations that were proposed, but never voted on, he would have been limited in how much fertilizer he applied in the fall. 

“Most farmers are already conserving water, conserving nitrogen on their own without having to put in any regulations,” said 63-year-old Makovicka, who typically fertilizes in the fall on some of the 800 acres he owns or leases. 

Farmers know nitrogen fertilizer is bad for the earth. Nitrogen turns into nitrate, which sits in the soil and slowly makes its way to Nebraska's groundwater — the source of drinking water for most residents of the state.  It’s the major source of contamination in Nebraska’s groundwater.

But, nitrogen is also needed to make crops grow in Nebraska. It’s necessary for Makovicka’s livelihood and that of hundreds of thousands of Nebraskans who work in agriculture. 

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York farmer Ron Makovicka changes an anhydrous ammonia tank on his farm near York. He applies fertilizer in the fall because it's easier and more efficient than a spring application.

Farming is the backbone of Nebraska’s economy, where one in four people work in agriculture-related jobs, and $6.4 billion in agricultural exports translate into $8.1 billion in economic activity, according to the state’s agricultural department.


Like many farmers, Makovicka says he has vastly reduced the amount of irrigated water he uses and the amount of nitrogen he uses. He uses watermark sensors in his corn fields so he knows when to irrigate and can check soil moisture levels on this phone. He applies an inhibitor, which can limit nitrate formation in the soil. 


A major cause of nitrates in Nebraska wells is fertilizer used on irrigated crops. 


While the amount of irrigation in Nebraska is declining, in 2012 Nebraska had the most irrigated acres in the whole country. There are 8.3 million acres of irrigated farmland in Nebraska — nearly 15% of all irrigated land in the country, according to USDA figures from 2012. 

Nebraska is the country’s third leading producer of corn for grain production and the fifth leading producer of soybeans, according to the state’s agricultural department.  

Those who study this problem say Nebraska farmers are doing a much better job of using only the fertilizer they need and cutting back on irrigation. 


But there’s a point of frustration for everyone: It can be difficult to track nitrate in the groundwater. 


Farmers ask: How can you tell if a reduction in fertilizer application is working? 


Soil types, topography and the depth to groundwater cause variance in recharge rates from the surface to the aquifer. 


Another confounding problem: It’s getting worse. 


According to a 2014 study that relied on well samples from 11,500 wells over 30 years, parts of Nebraska’s groundwater with nitrate levels above the federal limit continue to grow and new areas continue to emerge under irrigated cropland in the central and eastern parts of the state. 


And there’s more nitrate that hasn’t even reached the groundwater yet. 


This map shows the areas in Nebraska where the vadose zone — the area below the crop root zone, but before the groundwater — is contaminated with nitrate and other agrichemicals. Those are the contaminants that have not yet reached the groundwater.


This map created by the U.S. Geological Survey shows the relationship between nitrogen and the groundwater.

Water and fertilizer regulation

One complaint from Nebraska farmers: Too many regulations. 


But, the source of some of those regulations, the boards and managers at local Natural Resources Districts, say more needs to be done to protect the water, air and soil in Nebraska. 


Mike Sousek, the manager of the Lower Elkhorn NRD in Norfolk, which has enacted new regulations limiting fertilizer application, said the nitrate contamination is not getting better, despite years of regulations.


“Some of them have to change their practice. You hear complaints like, ‘This was a problem created 30 years ago. We are farming better now. It’s not happening now.’ That’s not what science is showing,” Sousek said. “There’s nitrates in the soil. …. We continue to add to this problem.”


Kyle Hauschild, the manager of the Little Blue NRD in Davenport, said nitrate contamination is on his radar.  


“We are trying to figure out what the best way to work with our producers (is),” he said. “A lot of it’s hard to undo what was done 40 years ago. All we can really do right now is try to do better and lessen the amounts of nitrates we put in the system.” 


In the 1960s, the Environmental Protection Agency set a federal drinking water limit for nitrate of 10 parts per million in part in response to cases of methemoglobinemia, sometimes called “blue baby syndrome," which affects oxygen transportation in the blood. In addition, nitrates are characterized as being “probably carcinogenic to humans" under certain conditions, according to the Centers for Disease Control.  University of Nebraska researchers are also studying possible nitrate links to the state’s high pediatric cancer rate. 


In Nebraska, the Department of Environment and Energy and the Department of Health and Human Services are charged with monitoring drinking water. There are about 99 community drinking water systems in the state that are being monitored because well samples have shown nitrate levels are rising, nearing unsafe levels or were high and are now being treated. 


At the local level, 23 local Natural Resources Districts regulate how much fertilizer farmers can apply and when as well as how much water they use. Nebraska’s NRDs — held up as a model around the country — have taxing authority, elected board members and are charged with protecting air, water and soil. 

In the mid-80s, Nebraska NRDs started creating groundwater management plans to deal with rising nitrate levels in the groundwater, according to this study.  This continues to this day. Some NRDs specify special management areas, such as the Bazile Groundwater Management Area, which covers 756 square miles and 21 communities in northeast Nebraska. 

The regulations in the Bazile are tiered based on contamination levels and vary by NRD. Some regulations include mandatory cover crops, irrigation scheduling, limits on spring fertilizer applications and nitrate testing reporting requirements.

Upper Big Blue General manager David A. Eigenberg said NRD boards must think about all residents, not just farmers.


“There is a tremendous concern on safe drinking water for all citizens of the district and sometimes we get caught up with the effect on agriculture, but one of our missions is to supply safe drinking water for all citizens of the district,” he said. 


Proposed regulations are not always received well. 


The Upper Big Blue NRD, which has 1.2 million acres of irrigated farmland, recently tried to limit fertilizer application to 120 pounds, among other things, but the backlash was so strong, the board backed down. It already prohibits fertilizer application before Nov. 1, requires annual reports and soil sampling in high-nitrate areas. 


At one meeting in September in York, first-generation farmer Mike Bergen joined about 300 other farmers who told the board the proposed rules had no science behind them or were not going to be effective. Bergen told the NRD board that he has already adopted split fertilizer application, uses moisture probes and is more efficient with water use. 


He called the regulations “complete government overreach.” 


Roger Houdersheldt, the Upper Big Blue board chairman who is also a farmer, said the backlash didn’t surprise him. 


“Nobody likes to be told what to do,” he said. “It’s just we need to figure a way to handle this problem with the least amount of regulation possible.” 

What farmers are doing

For many, using less fertilizer is a matter of economics. With low corn and soybean prices, the 2019 spring floods and the trade war with China, many farmers are operating with thin margins. They can’t afford to overspend on fertilizer. 


At the local level, many farmers work closely with NRDs to institute best management practices and take part in pilot projects and demonstration sites. In addition, the state’s extension agents and university researchers work with farmers. 


York farmer Ron Makovicka is doing a study with the University of Nebraska-Lincoln on the use of a nitrate inhibitor product called N-Serve, which is supposed to stabilize nitrate in the soil. Some NRDs require the use of N-Serve or another inhibitor, but some farmers say it’s too corrosive or not effective.


In McLean in northeast Nebraska, farmers John and Dan Schmit spent $380,000 on an Exactrix machine to apply fertilizer components such as anhydrous ammonia in the ground with other chemicals where they will crystalize and be less likely to leach. 


They are exempt from some of the Lower Elkhorn NRDs fertilization application regulations so they can experiment with new technology that uses less fertilizer than conventional methods without affecting yields. 


To control nitrates, NRD regulations focus on water and fertilizer use. Here are a few examples.


The Lower Elkhorn NRD limits farmers to 80 pounds of fertilizer per application and requires soil sampling regardless of nitrate levels and use of an inhibitor, which is a nitrogen stabilizing agent. The NRD provides funds to subsidize costs of soil sampling. 


In the Central Platte NRD, most applications of fall fertilizers are prohibited. The Central Platte NRD is held up as one example where nitrate management and control has reduced nitrate levels in the groundwater. Nitrate levels were increasing at 0.5 parts per million and reached 19 parts per million in 1987, according to this NRD report. The NRD started requiring soil sampling, nitrogen credit application and more reporting by farmers. Levels decreased to 13.5 parts per million by 2018, said Central Platte NRD manager Lyndon Vogt. 

*The Central Platte NRD has never required flow meters. A previous version misstated information about the use of flow meters. 

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Farmer Jay Meyer of Daykin inspects his soybean field after a hailstorm. Meyer is a board member of the Little Blue NRD, which sets fertilizer and water use regulations for farmers.

Joe McReynolds, who farms 1,400 acres near Edgar, estimates he uses 20% to 25% less fertilizer than he did 10 years ago. He does soil sampling, uses electronic sensors for irrigation and applies fertilizer at a variable rate.


“We’ve gotten a lot more education, so that’s good so we know, OK we can cut back on things and still be effective in what we can produce,” McReynolds said. 


The Central Platte NRD is planning a four-year, $320,000 study this fall with farmers that will examine the effects of cover crops on groundwater contamination. Cover crops such as rye can prevent nitrate leaching and improve soil health, thus resulting in less fertilizer run-off. 


“We are hoping this study shows the increased soil quality that we get from cover crops increases our holding capacity and we are seeing less runoff,” Vogt said.  


The Little Blue NRD in Davenport is taking part in research on vadose zone sampling, said Daykin farmer Jay Meyer, who is a board member. 


“We don’t want to impose a bunch of rules and not know if it’s going to do any good,” Meyer said. “If we are going to have rules, we hope they do what we want them to do. And not just restrict the farmer for no reason."

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Aaron Zimmerman (left) helps his brother Ryan Zimmerman as they apply chicken manure as fertilizer on their farm in Pierce. The Zimmermans are converting all 2,200 acres of their farm to organic.

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Pierce farmer Aaron Zimmerman got sick of working with toxic chemicals.

Some Nebraska farmers are deciding to stop using synthetic fertilizer on their own. 

More and more Nebraska farmers are converting portions — or even all — of their operations to organic. The number of Nebraska farms with organic operations increased from 159 to 277 between 2012 and 2017, a 74% increase, according to USDA agriculture census data released in April 2019.


Nationally, organic farming operations increased 39% to 17,741 farms.  Organic farmers cannot apply synthetic fertilizer. 

Aaron and Ryan Zimmerman are converting all their 2,200 acres in Pierce to organic. They are in the second year of a three-year process. They are converting for economic reasons — corn and soybean prices are already so low — but mostly environmental. The breadth of agrichemical application is staggering, they say.

“You look at all the chemicals that are going on the fields and into our food supply it’s like man this is just us and we’re nothing, we’re a small speck,” said Aaron Zimmerman, who is married with children and lives on the farm. “It’s always kind of bugged me, the way I farmed. It would affect me.  I would feel like crap certain times of the year when I’d be working with chemicals and it was kind of wearing on me.” 


Ryan Zimmerman, who also experienced health problems he attributed to farm chemicals, said this problem will take a long time to fix.


“A lot of it is a lot of farmers are doing a good job of just being more proactive, but it’s one of those deals it’s just going to take a long time to right the ship,” he said. 

Corn and soybeans on Ron Makovicka's farm in York. Makovicka is growing different test varieties of seeds. 

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