John Duarte, a fourth-generation California farmer, was disappointed this week when President Trump's repeal of the Waters of the United States rule didn't translate into immediate legal relief from an Obama administration's environmental case against him.

Duarte says he has spent $2 million and five years fighting charges that he violated provisions of the Clean Water Act by plowing too deeply on watery areas of a 450-acre parcel of land he purchased to grow winter wheat for at least one year.

The Army Corps of Engineers ignored evidence that showed that he had not tilled the land too deeply, he said, as well as evidence that the vernal pools—the wetlands in questions on the property—remain healthy.

A California U.S. District Judge ruled against Duarte last year, and he faces a $2.8 million fine and potentially tens of millions of dollars more in environmental mitigation when the case goes to trial in mid-August.

"I watched the Trump speeches and the WOTUS rule repeal come through, and even on election night we thought we saw the clouds part and the sun come through," Duarte said.

"[Federal prosecutors] could just settle the case with us for a stipulated amount. Obviously, I believe that should be a low amount, and that's what we believe would be consistent with Trump policy" when it comes to the Waters of the United States Act, or WOTUS repeal, he said.

The case, which has become a rallying cry for conservatives and farmers across the country, will have a precedent-setting impact on law, lasting far longer than any one administration's agency policy or directive.

Trump has the opportunity to protect farmers or open them up to more environmental lawsuits in the future, Duarte said.

"This case is an opportunity and a threat—and it all depends on how the current administration handles it," he said. "I think it's clear President Trump doesn't want to punish farmers for farming, and there's still some long-term swamp rats that want to pursue the past administration's policies."

A spokesman for the Justice Department said he could not comment on any active litigation.

Since Trump's election, both sides have squared off over the issue.

Vernal pools, such as those on Duarte's property, are seasonal depressions that are covered by shallow water for "variable periods" from winter to spring but may be completely dry for most of the summer and the fall, according to the EPA website. The pools, which the agency says are increasingly threatened, provide "unique habit for numerous rare plants and animals that are able to survive and thrive in them."

If Trump sides with Duarte, environmentalists argue such a decision could jeopardize that protection of millions of acres of wetlands and streams.

But conservatives and property-rights advocates dismiss dire predictions, arguing that Congress never intended to target farmers when they passed the Clean Water Act to protect the countries lakes, streams and navigable waters.

Duarte's supporters argue that the Clean Water Act and WOTUS both have exemptions for "normal" farming activities like plowing, grazing and mowing they believe should apply to Duarte's case.

Duarte's advocates in Washington are helping him make his case.

House Agriculture Committee Chairman Michael Conaway (R., Texas) and Judiciary Committee Chairman Bob Goodlatte (R., Va.) penned a letter in late May to Attorney General Jeff Sessions urging him to review the Justice Department's case against Duarte.

Sen. Joni Ernst (R., Iowa) also pressed EPA Director Scott Pruitt about Duarte's case during his confirmation hearing earlier this year against the backdrop of a large photo of Duarte's farm. She specifically asked Pruitt if the Trump administration would "stop trying to regulate ordinary farming practices."

"Yes, senator," Pruitt replied.

But it wasn't the EPA that brought the case against Duarte or first stepped onto his property to scrutinize the plowing. Former EPA Gina McCarthy had repeatedly defended her agency's WOTUS rule by telling Congress it would abide by the same "normal farming exemptions" found in the Clear Water Act.

Five years ago, a U.S. Army Corps of Engineer field inspector was driving by the land in question and noticed a large tractor working the fields and suspected it was violating the Clean Water by "deep ripping" the land, digging holes three-to-seven feet deep and depositing the dredged soil into the vernal pools. The "deep-ripping" process is commonly used for orchard or vineyard planting, not the wheat field Duarte was planting.

Duarte said he presented evidence that the tilling only went four to seven inches deep, and possibly a foot deep in a few places, complying with the law. He also argues that it didn't threaten the health of the protected vernal pools on the property.

"No deep ripping took place," Duarte said in court documents.

Duarte and his team of lawyers take particular exception to several Army Corps descriptions in the its court filings about the alleged damage to the vernal pools the plowing had caused, including a line that the tilling created "mini-mountain ranges" five inches high that could harm the vernal pools nearby.

The California U.S. District Judge who ruled against him in a summary judgment last year, he said, "has blown by" the exclusions in the Clean Water Act for farming, and specifically for plowing.

"I'm still trying to figure out how a plowing method that doesn't not move soil," Duarte said, referring to the Army Corps arguments in the context of the Clean Water Act farming exemptions. "Nobody is advertising a plow that doesn't move soil."