Preserve Our Islands (POI) has taken its decade-long battle against Glacier Northwest to federal court, claiming the agencies overseeing the corporation’s expansion plans are failing to safeguard the region’s imperiled killer whales and other animals protected under the Endangered Species Act.

In a 21-page lawsuit filed in U.S. District Court last week, the Vashon-based group, along with two other conservation organizations, alleges that three federal agencies have violated federal law and acted “capriciously and arbitrarily” in approving Glacier’s proposed barge-loading pier.

The other two groups are People For Puget Sound and the Washington Environmental Council.

In particular, they note, the National Marine Fisheries Service and the U.S. Fish and Wildlife Service have failed to uphold their responsibilities under the Endangered Species Act and other federal laws. The groups also take issue with the U.S. Army Corps of Engineers, which recently gave Glacier the permit it needed to build the pier without requiring the corporation to undertake a more exhaustive environmental review.

The pier — from its construction to its size, covering more than 7,500 square feet of water surface — could harm killer whales, humpback whales, Puget Sound chinook and Puget Sound steelhead, all of which frequent the waters off Maury, the suit alleges.

The suit was triggered by the Corps’ decision in July to issue Glacier a permit to build the pier, one of the last administrative hurdles the corporation had to overcome to go forward with its controversial plans. It marks POI’s first foray into federal court.

“Our decision (to sue) is not because we don’t like the decision the Corps made. It’s based on the fact that they ignored the science,” said POI president Amy Carey.

Carey said POI and other conservation groups gave the Corps ample scientific data showing how the pier and the traffic it would generate will likely harm killer whales and other protected species.

“But you see (in the Corps’ documents) that they have frequently taken Glacier’s talking points and documents verbatim as the basis for how they’re supporting their decision,” she said.

Patricia Graesser, a spokesperson for the Corps, disputed Carey’s contention.

“We did an independent analysis. We did a thorough environmental assessment. And that information is documented,” she said.

Graesser added that the Corps’ decisions on high-profile projects of-ten get appealed by advocacy groups. Its permit for the third runway at the Seattle-Tacoma Inter-national Airport and the building of new sports fields at Magnuson Park, for instance, were both appealed, she said. In both cases, the Corps’ decision was upheld, she added.

Pete Stoltz, Glacier’s permit coordinator, also said it was not a surprise to the company that the groups appealed.

“We’re confident that all the agencies took a very close look and did a thorough job of reviewing the project,” he said, adding, “We expect that (opponents) will pursue every opportunity to appeal, and this is one of the opportunities.”

The suit comes at a critical time for the region and its top policy makers, many of whom have focused increasing attention on the health of Puget Sound; Gov. Christine Gregoire has called the Sound’s restoration and protection one of the area’s top conservation priorities.

It also marks the first legal action on behalf of southern resident killer whales since the iconic animal was listed as endangered in 2006.

Those involved with the lengthy effort to get the region’s orcas protected under the Endangered Spe-cies Act, considered the strongest federal environmental law on the books, say it’s disheartening to now see federal agencies sidestep its enforcement.

“It’s enormously frustrating to see all the effort that goes into listing a species as threatened or endangered and then, when the projects and permits come through, see the agencies fail to say, ‘Wait a second,’” said Kathy Fletcher, executive director of People For Puget Sound.

“You don’t list them on one hand and destroy their habitat on the other,” she added.

The lawsuit takes aim at the three agencies for their alleged violations of several laws, including the National Environmental Policy Act, the Marine Mammal Protection Act and the ESA.

The government’s recovery plan for the region’s killer whales, for instance, found the animals are on decline because of elevated underwater noise, insufficient prey and the growing incidents of whale-vessel interaction, the suit notes. And yet the Corps issued Glacier a permit despite evidence that construction and operation of the pier would create more underwater noise; that the pier’s shade would hurt eelgrass beds and, in turn, the small fish — or orca prey — those beds support; and that the dock would create a physical barrier for these wide-ranging animals, the suit says.

According to the suit, the Corps also failed to address the project’s impact on the forested uplands Glacier owns, where arsenic-laden soil would have to be removed, as well as the project’s impact on recreational use, property values and aesthetic values.

“The Corps’ public interest evaluation failed to adequately consider the true economic costs of the proposal and failed to balance the project’s economic costs against its economic benefits,” the suit contends.

But even with the filing of the suit, officials say, Glacier has all the permits it needs to move forward on its pier, once the state Department of Natural Resources (DNR) gives the corporation a lease to the state-owned tidelands that surround Glacier’s property. DNR is currently reviewing Glacier’s project to ensure it meets a state-issued management plan for those tidelands, which make up what’s called the Maury Island Aquatic Reserve.

According to Patricia O’Brien, an assistant attorney general who oversees legal matters for DNR, the state agency can continue its review process and, if it so decides, issue a lease, even with the pending federal lawsuit.

The state can issue a lease only if Glacier has all of its permits, she noted. “And right now, it does,” she said.

Carey, though, said she doesn’t believe Glacier has what would be considered “a final permit” with the lawsuit now hanging over it and questioned the wisdom of DNR moving forward in light of the latest skirmish.

“It seems it would be prudent for them to wait for this issue to be resolved,” she said.