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A killer whale breaches the water as two adults and a younger whale move on the waters of the Salish Sea west of Pender Island, B.C., on April 20, 2015.

DARRYL DYCK/The Globe and Mail

Environmental groups are celebrating a Federal Court of Appeal decision that quashed Ottawa’s approval of the proposed Trans Mountain pipeline expansion, saying the ruling highlights government obligations to protect species at risk – in this case, southern resident killer whales.

But the long-term impact of the court ruling on the killer whales is unclear. The federal government insists the Trans Mountain expansion, which would roughly triple the capacity of an existing pipeline system that runs from near Edmonton to the B.C. coast, will go ahead despite the court setback. For now, however, the whales have been thrust into the spotlight, raising hopes that more can be done to save them from extinction.

“This decision ... means we hold the line on the conditions within the Salish Sea not getting worse," said Misty MacDuffee, a biologist with Raincoast Conservation Foundation.

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Raincoast and Living Oceans Society were joint applicants in a consolidated legal challenge to Ottawa’s approval of the proposed Trans Mountain pipeline expansion.

On Aug. 30, the Federal Court of Appeal quashed Ottawa’s approval of the project, citing shortcomings in the government’s duty to consult with First Nations and a decision by the National Energy Board to exclude project-related tanker traffic from its review.

That unjustified exclusion led to “successive, unacceptable deficiencies in the Board’s report,” the court said, including a failure to fully account for risks to southern resident killer whales.

That was a win for environmental groups, which had argued the NEB erred in how it defined the scope of the project.

“We maintained the [NEB] truncated a review of the pipeline and marine shipping to end the project at tidewater after they realized they would be violating the Species at Risk Act by going ahead with the project,” Ms. MacDuffee said.

Southern resident killer whales have been listed as endangered under Canada’s Species at Risk Act since 2003. By defining the expansion to not include project-related marine shipping, the board failed to consider its obligations under that legislation to mitigate any impact with respect to southern resident killer whales, the court said.

And although the federal government’s commitment to a proposed action plan for the southern resident killer whale and a previously announced Oceans Protection plan is laudable, such “inchoate initiatives” don’t make up for shortcomings in the board’s report, the court said.

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The court ruling “will give the time for the government to demonstrate what measures are being put into place so that should [Trans Mountain] go ahead, there is a better sense people have been consulted and people fully understand the risks,” said Andrew Trites, a marine mammal researcher at the University of British Columbia.

Mr. Trites said he is less worried about the impact of vessel traffic noise on southern resident killer whales than the impact of an actual oil spill, which he called a “catastrophic” possibility, explaining that it could result in the whales breathing in oil.

Southern resident killer whales' territory ranges from southeastern Alaska to central California, showing up in summer in waters between Vancouver Island and Washington state. Threats include reduced availability of prey, increased pollution and shipping noise that can interfere with the whales' ability to hunt and communicate.

The animals' current prospects are poor, with females producing more male than female calves and having fewer calves over all.

“They used to calve every five years – now it’s every 10 years,” said Ken Balcomb, founder of the Center for Whale Research in Washington state.

Mr. Balcomb, who has been studying southern residents since 1976, said he’d like governments to pay more attention to watersheds to improve conditions for Chinook salmon, a key food source for the whales.

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Much of the debate around Trans Mountain has focused on tanker traffic. Under the proposal, the number of tankers leaving the Westridge terminal would rise to 34 a month from about five now. The NEB estimated that project-related vessel traffic would amount to a maximum of 13.9 per cent of all boat traffic in the regional study area and would decrease over time – a forecast that reflects expectations that the waters in the area will get busier with or without Trans Mountain.

Thursday’s court ruling sets a helpful precedent, said Dyna Tuytel, a lawyer with Ecojustice who represented Raincoast and Living Oceans Society in the Trans Mountain case.

“I think it’s a really important piece of that bigger picture of the current struggle of the southern residents," Ms. Tuytel said.

"We saw in May that the ministers of fisheries and oceans and of environment acknowledged that the species is facing imminent threat to its very survival, and an acknowledgement that something needs to be done for them,” Ms. Tuytel said in an interview.

The federal government in May announced fishing restrictions on Chinook salmon, citing an “imminent threat to both survival and recovery” for southern resident killer whales.

Raincoast and other environmental groups earlier this year called for an emergency order under the Species at Risk Act.

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