ELK RAPIDS, MI — A federal judge has ruled that a northern Michigan food processor illegally polluted wetlands and tributaries that ultimately drain to Lake Michigan, handing conservation groups and tribes a landmark clean water victory.

In a Nov. 12 opinion, U.S. District Judge Jane Beckering found Burnette Foods liable under the Clean Water Act for discharging pollutants into wetlands connected to Spencer Creek, a groundwater-fed tributary that drains into Elk Lake and ultimately Grand Traverse Bay.

Beckering granted summary judgment to a group of plaintiffs led by the Watershed Center Grand Traverse Bay, who sued in 2023 alleging that wastewater sprayed on fields near Elk Rapids was seeping into wetlands and surface waters without a discharge permit.

In a 40-page opinion, Beckering concluded that the adjacent wetlands qualify as “waters of the United States” under the U.S. Supreme Court’s 2023 Sackett v. EPA decision, and that Spencer Creek is a protected tributary because it is a relatively permanent stream.

The decision makes Burnette liable for violations of the federal Clean Water Act and the Michigan Environmental Protection Act. The case now shifts to a remedies phase, where the court will decide what corrective actions or penalties the company must take.

Burnette’s attorneys declined to comment.

Christine Crissman, director of the Watershed Center, said the ruling validates years of monitoring, records review and complaints that failed to stop the pollution.

“We’ve been engaged in this for over five years and the order that Judge Beckering issued basically sided with the facts we had,” Crissman said. “We’re pretty ecstatic.”

Crissman said her group sued only after years of state violation notices failed to stop the pollution.

“They were violating their groundwater discharge permit and we also believed they were discharging to surface waters without a permit,” Crissman said. The state “had done several site visits and issued notices of violation, but none of it stopped the pollutants from reaching the groundwater and the wetlands and the stream.”

Beckering’s ruling “is sort of the first step,” Crissman said, with the next stage focused on “making something happen that’s going to keep pollutants from entering the water.”

The lawsuit was among the first filed after the U.S. Supreme Court’s 2023 Sackett v. EPA ruling sharply restricted which wetlands qualify for federal protection. Crissman said the lack of case law made the legal landscape uncertain when the groups filed.

“When we filed the suit, it was right after that Sackett decision came out… and there was very limited case law,” she said. “We relied fairly heavily on a case in Hawaii,” referencing the Supreme Court’s 2020 County of Maui ruling on groundwater-connected discharges.

Even under the narrower standard, Crissman said, “we always felt like the waters were connected and should be considered ‘waters of the United States,” also known as “WOTUS.”

Beckering agreed, finding that the wetlands next to the spray fields are part of a connected system and therefore federally protected.

In Elk Rapids, Burnette Foods processes and packages fruit and vegetable products such as cherries, apples, beans, and other produce for distribution to food manufacturers and retail brands. The company also has locations in East Jordan, New Era and Hartford.

According to case documents, Burnette’s Elk Rapids plant sprayed high-strength wastewater on roughly 49 acres of nearby hay fields fields under a groundwater discharge permit.

The Michigan Department of Environment, Great Lakes and Energy (EGLE) issued Burnette violation notices in 2019, 2020, 2021 and 2023 documented over-saturation, ponding and wastewater flowing off the fields into adjacent wetlands and Spencer Creek.

Burnette’s self-reported discharge reports also showed numerous violations of daily and weekly application limits starting in 2018.

Sampling by EGLE and consultants detected rising concentrations of nitrogen, phosphorus, chloride, potassium, manganese, iron and biochemical oxygen demand in groundwater beneath the spray fields. In 2021 and 2023, EGLE found elevated E. coli in both Burnette’s wastewater and the wetland where Spencer Creek forms.

Private landowners also reported foam, creek discoloration and odors.

Earlier this year, the state notified Burnette that the site qualifies as a Part 201 cleanup facility under Michigan’s environmental remediation law and directed the company to submit a work plan to investigate the extent of groundwater contamination.

In court, Burnette argued that the spray-irrigated fields are agricultural operations exempt from the Clean Water Act and that Spencer Creek is too intermittent to qualify as a federally protected tributary. Beckering rejected both points, finding that the wastewater remained industrial in nature and that the creek and wetlands together form a connected hydrologic system that drains directly into Elk Lake.

Beckering’s opinion credited expert testimony and monitoring data showing that the wastewater does not simply soak in and disappear but moves through shallow groundwater into nearby wetlands and Spencer Creek in a relatively short time with a detectable pollution signal. That combination, she found, makes the groundwater discharge the “functional equivalent” of a pipe discharging directly into protected waters.

The ruling comes as environmental groups are raising alarms about a new U.S. Environmental Protection Agency proposal under the Trump administration that would further limit federal wetland protection in the wake of the Sackettdecision.

Advocacy groups say the rule proposed Nov. 17 would tighten the definition of “waters of the United States” even more — potentially excluding seasonal streams and many wetlands that lack year-round flow or an uninterrupted surface connection.

“Today, the Trump EPA is giving polluters a free pass to dirty our waterways by rolling back protections for important sources of clean water that Americans need,” said Nancy Stoner, senior attorney for the Environmental Law and Policy Center.