Republican Senate candidate John Raese filled in wetlands and damaged more than 2 miles of streams when he rerouted them to create waterfalls on a private, 18-hole West Virginia golf course that federal regulators say he built without the required permits.

The years-long construction of Pikewood National Golf Club near Morgantown is “probably the biggest violation we’ve ever seen in this district,” Sheila Tunney, spokeswoman for the U.S. Army Corps of Engineers in Pittsburgh, told The Associated Press.

More than two years ago, the Environmental Protection Agency ordered Raese, the club’s president, to develop a plan to mitigate the damage. Tunney says work on that plan is ongoing.

Raese, who’s challenging incumbent Democrat Joe Manchin, recently called Pikewood “the nicest golf course in the United States” and a local job creator.

“EPA believes that several years ago, Pikewood National Golf Club disturbed some wetlands or other areas technically considered to be ‘waters of the United States’ under the federal Clean Water Act,” Greer Industries vice president and general counsel J. Robert Gwynne said in a statement Monday afternoon. Raese is the president and chief executive of Greer, a steel and limestone producer.

“Pikewood believed it had complied with all applicable laws at the time of its construction activities and is working with the EPA to resolve all outstanding issues,” Gwynne added.

Raese, himself, did not respond to a request for comment.

The millionaire businessman campaigns routinely on a platform that includes abolishing several federal agencies, including the EPA, and the government regulations that he says squelch economic development.

EPA officials have repeatedly declined to answer questions about the violations but did provide the AP a copy of a six-page compliance order issued in March 2010. The last page says EPA “reserves the right to seek any remedy available under the law,” including pursuit of any civil or criminal charges it deems appropriate.

Tunney said the corps first learned about the 1,300-acre golf course, which sits on the Monongalia-Preston county border, from a farmer who complained he was no longer getting water from a local stream.

The course took several years to build, and aerial photos show the waterfalls are at the par-3 fifth hole, dubbed “Mow Green.” The website describes it as a small, peanut-shaped green with a limestone ledge on one side and a “reflection pond” on the other.

“Designed to fit the lay of the land, Pikewood National has a natural look,” its website proclaims. “In fact, the only earth that was disturbed in the making of this course was that used to build greens and tees, and the rest of the land is allowed to lie as God intended it.”

But the corps says the waterfalls and ponds are not natural; they were created by rerouting waterways.

“I can only assume what they mean is they kept the natural forest around it, which they did,” said Jon Coleman, a project manager in the corps’ regulatory branch who has been investigating the work since mid-2009.

In all, the construction diverted, buried or otherwise disturbed nearly 2.3 miles of streams and about one-seventh of an acre of wetlands, Coleman said. Workers also built dams that disrupted Laurel Run, a tributary of Deckers Creek.

“The ponds and stuff, those are some of the big violations,” Coleman said. Damming a waterway not only changes the quality of the water but has the potential to dry up downstream areas.

Reconstructing the damage is difficult, he added, because it occurred so long ago.

“It’s like an autopsy,” Coleman said, only with tools including historical maps and satellite imagery.

By law, Raese should have sought a permit to place dredge and fill material in waterways under Section 404 of the Clean Water Act, the same section mining companies use. As a quarry owner, Raese would be familiar with such permits.

There are two kinds of 404 permits, a nationwide or general permit typically used for projects that are smaller and have little environmental impact. Those permits are free, but analyzing the project and coming up with strategies to minimize harm typically takes 45 days, Coleman said.

An individual permit, which has more in-depth requirements and includes a 30-day public notice provision, would have cost $100 and taken about 120 days to obtain.

Raese hinted at the problems with Pikewood last week while calling again for abolition of the EPA, suggesting during a Shepherdstown debate that the agency and the corps are trying to punish him. He accused the EPA of “terrorizing business” and offered Pikewood — which he did not mention by name — as an example of valuable job creation.

“You know what happens to me?” he said in the debate. “Right now, the EPA and the Army Corps are my new partner because they’re up there every day. Fines. Looking at me, for what? I don’t know. I built it on 1,300 acres and they’re looking at probably 20 feet by 30 feet.

“Can you imagine this, when you try to create something that’s so beautiful and so pretty and has won so many awards?” he added. “My award is that I’m chastised by government.”

Golf Digest rated Pikewood the best new private course of 2009, noting its membership “initiation fee” is $30,000.

According to Links magazine, Raese and Gwynne designed and built the course themselves rather than hire an architect.

“We wanted to feature the natural terrain and the rock formations on the property,” Gwynne told the magazine. “After all, we are in the rock business. We wanted to make the most natural course we could.”

Raese is also chairman of the board of West Virginia Radio Corp. and the MetroNews radio network, and vice president of the company that publishes The Dominion Post newspaper.

This is Raese’s  fourth Senate bid. He challenged Sen. Jay Rockefeller in 1984 and the late Sen. Robert C. Byrd in 2006. In a special election to fill Byrd’s unexpired term after his death in 2010, Raese lost to Manchin by 10 percentage points.

Now Manchin and Raese are competing for a full term.