Fed Court Upholds Irrigation Exemption

LINCOLN, Neb. (DTN) -- A federal appeals court ruled a key grassland bypass project in California does not need a Clean Water Act permit. Fishing and environmental groups had alleged in a lawsuit that the project does not qualify for an agricultural exemption.

The U.S. Court of Appeals for the Ninth Circuit at the end of last week upheld a lower court's ruling of summary judgement in favor of the U.S. Bureau of Reclamation and the San Luis and Delta Mendota Water Authority in California.

The California Grassland Bypass Project is a project launched in 1996 to address selenium contamination from ag drainage of about 97,400 acres of farmland in central California. The project diverts selenium-contaminated subsurface drainage water away from irrigation canals and wetlands by using the San Luis drain to move the water to the San Joaquin River.

The project has been operating without a National Pollutant Discharge Elimination System permit since 1997.

In a lawsuit originally filed in 2011 by the Pacific Coast Federation of Fishermen's Associations Inc., California Sportfishing Protection Alliance, Friends of the River, San Francisco Crab Boat Owners Association Inc., and the Institute for Fisheries Resources, the groups argued the project needed a CWA permit because its discharge contained pollutants from non-ag sources.

Those sources include groundwater seepage from non-irrigated land, runoff from highways, residences and other non-irrigated areas, accumulated sediment in the drainage system and runoff from a solar panel installation on retired farmland.

The CWA does not require permits for discharges that are composed entirely of return flows from irrigated agriculture.

The three-judge panel of the Ninth Circuit agreed with a ruling by the U.S. District Court for Eastern District of California.

"Plaintiffs' theory does not follow from the text and is inconsistent with the purpose and structure of the CWA, and as a practical matter would render the irrigated agriculture exemption a dead letter," the Ninth Circuit panel said in its opinion handed down on Sept. 5, 2025.

"Under plaintiffs' reading of the statute, an irrigation system would have to ensure that no windblown dust ever enters the return flow conveyance for the return flow to qualify under the statutory exemption -- a scientific impossibility. Plaintiffs have not been able to explain how any irrigated agriculture system would ever qualify for the exemption."

The Family Farm Alliance and other agricultural groups joined the case as amicus curiae, supporting the U.S. Bureau of Reclamation, San Luis and Delta-Mendota Water Authority and Grassland Water District.

In briefs filed with the Ninth Circuit, those groups pointed out how the broad scope of irrigated agriculture makes it impossible to exclude diffuse, nonpoint source pollutants.

"This is a complete win for agriculture," Norm Semanko, Family Farm Alliance general counsel, said in a news release.

"The Ninth Circuit confirmed what Congress intended nearly 50 years ago: Irrigation return flows are exempt from federal permitting, provided they don't include other unrelated point-source discharges."

As a result of the ruling, irrigation return flows discharged to waters of the United States through agricultural drains remain exempt from Clean Water Act NPDES permits, unless those drains accept pollutants from unrelated and unpermitted point sources such as municipal stormwater or industrial effluent.

"The Family Farm Alliance will continue to monitor the case should the plaintiffs seek further appeal," Semanko said. "For now, the Ninth Circuit has reaffirmed a key protection for irrigated agriculture, ensuring farmers and water districts can focus on producing food and fiber rather than navigating unnecessary federal permits."

In the amicus brief filed by the agriculture groups, they said that losing the irrigation exemption would have had broad implications for farmers in the West.

"Such a ruling would broadly affect western agriculture, forcing thousands of farmers and operators of agricultural drainage systems across the western United States to immediately apply for and operate under onerous NPDES permits or face liability under the CWA," the groups told the Ninth Circuit.

"The theories advanced by appellants in this case threaten to undermine congressional intent and erode CWA exemptions, all in an effort to subject irrigated agriculture to the CWA's NPDES permitting and regulatory requirements that were intended and designed for altogether different situations such as municipal wastewater plants or factories."

Todd Neeley can be reached at todd.neeley@dtn.com

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