Spenser Heaps, Deseret News
FILE - Algae bloom at Utah Lake July 15, 2016. Utah spent a relentless summer and protracted fall suffering from multiple harmful algal bloom outbreaks, an escalating threat to U.S. waterways that include the Mississippi River and Lake Erie.

SALT LAKE CITY — Utah spent a relentless summer and protracted fall suffering from multiple harmful algal bloom outbreaks, an escalating threat to U.S. waterways that include the Mississippi River and Lake Erie.

Throughout much of Utah, a dozen lakes, reservoirs and ponds were infested this year with blue-green algae, or cyanobacteria, that can sicken people and kill animals.

Agricultural runoff is a key culprit in many instances that lead to the proliferation of nutrients like phosphorus and nitrogen, which contribute to the outbreaks.

The nexus of agricultural operations and onset of the green scum led the Associated Press to examine the effectiveness of voluntary financial incentives offered by the U.S. Department of Agriculture to boost water quality.

The analysis showed that from 2009 to 2016, Emery and Box Elder counties were among the nation's top five recipients of $1.8 billion in federal funding designed to cut nutrient and sediment runoff, or otherwise improve water quality.

Over that period, Emery County received $11 million and Box Elder County got $9 million. Neither county is a hot spot for algal bloom outbreaks, though Box Elder County's Mantua Reservoir suffered an infestation this year.

Utah County, home to Utah Lake, the state's largest freshwater lake frequently infested, received just shy of $776,000 over the same time frame.

State water quality regulators do not believe agricultural runoff is the root cause of Utah Lake's algal bloom problem, instead targeting wastewater treatment plants to reduce nutrient pollution, establishing a technology-based limit for phosphorus that facilities must meet by 2020.

Erica Gaddis, director of the Utah Division of Water Quality, said regulators are also identifying new nutrient pollution limits for other waterways throughout the state, establishing a tiered system that goes after the most critical water bodies first.

The state Department of Environmental Quality estimates that 43 percent of Utah's lakes and reservoirs are nutrient-impaired, and nearly half of the state's rivers will degrade in water quality over the next 20 years.

Federal funding offered through the U.S. Department of Agriculture's Natural Resources Conservation Service is part of a broader spectrum of voluntary incentives designed to boost more environmentally friendly practices among farming and ranching operations, which contribute to nutrient pollution.

In its analysis, the Associated Press questioned the effectiveness of voluntary programs — including the Environmental Quality Incentives Program, or EQIP. It also noted the low participation rates on a national scale, just 6 percent of an estimated 2 million farms.

"We've had decades of approaching this issue largely through a voluntary framework," said Jon Devine, senior attorney for the Natural Resources Defense Council, a New York-based, nonprofit environmental advocacy group. "Clearly the existing system isn't working."

Jay Humphrey, manager of the Emery County Water Conservancy District, disagrees.

"You don't have to twist anybody's arm to participate. These individuals who want to see improvement and efficiencies are usually standing in line," Humphrey said.

Over the years, farmers served by Huntington, Ferron and Cottonwood creeks have all moved to pressurized irrigation systems instead of using flood irrigation techniques, with assistance from federal programs like EQIP, he said.

"We know the program is working," Humphrey said, noting that the fourth creek, Muddy, is transitioning as well.

In Emery County, the federal funds aren't targeting agricultural runoff to prevent algal bloom outbreaks, instead focusing on reducing salinity in tributaries to the Colorado River.

Humphrey said piping irrigation systems directly to a farmer's operation to use sprinklers instead of flood irrigation reduces the salinity in return flows to rivers by as much as 50 percent.

The U.S. Bureau of Reclamation instituted an expansive program to curb the salinity problem in the Colorado River to meet water delivery and water quality obligations to downstream users and Mexico.

"If we can improve the water up here, it is a whole lot cheaper than to try to do it in Yuma or Mexico or pay for those damages," Humphrey said. "If we are cleaning up the rivers all the way from the Green and San Rafael rivers to the Colorado into Mexico, then that is not a bad deal. I think it is a win for the environment, a win for the water users and a win for the federal government."

Pedro Ramos, the Natural Resources Conservation Service's basin resource coordinator in Utah, said EQIP funding is used in a variety of resource improvement projects, including rangeland health, helping sage grouse and conducting sediment control, which is where Box Elder County primarily directed those monies.

"We have seen the changes on the landscape already with better irrigation systems, more efficiently used water. As it runs through field after field after field, that water is picking up sediment along the way and water quality degrades. It is addressing problems like that," Ramos said.

The AP analysis underscores the complexity of the algal bloom problem, which Utah regulators say has to be addressed in a multifaceted approach, especially as unique waterways like an urban pond in Ogden and high mountain reservoirs like Strawberry suffer outbreaks.

Utah's water quality and agriculture agencies work with farmers, ranchers and water delivery systems to boost nutrient reductions, but Gaddis said combatting wastewater effluent, storm runoff and agriculture runoff is costly and complicated.

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The Utah Conservation Commission, for example, includes multiple partners working to improve the water quality at Utah Lake. In particular, agencies teamed up for the Wallsburg Project to remove phosphorus from a stream that drained into Deer Creek. It was an expensive project and took years to complete.

Regulators acknowledge more needs to be done, especially in light of the potentially stunning consequences to the vitality of Utah's waterways, which contribute as much as $2.4 billion to the economy from recreational activities like angling and boating.