Specifically, Justice Eleanor Dawson wrote in the court's Thursday decision that the National Energy Board, which was responsible for reviewing the project prior to government approval, didn't properly account for oil tankers that would be brought to the Pacific coast of British Columbia to take the oil from the pipeline.
In its decision, the court also said the federal government failed to meet the minimum standard required in its consultations with Indigenous people. The court also concluded that the federal government failed in its duty to engage in meaningful consultations with First Nations before giving the project the green light.
The court decision means that federal approvals of the pipeline project are essentially quashed until the issues of consulting First Nations are adequately addressed.
Canadian Prime Minister Justin Trudeau approved the project - then in May nationalized it in an attempt to ensure the pipeline expansion would be built, despite extensive controversy on both sides of the border.
The company's shareholders voted on Thursday morning to approve the $3.5 billion ($4.5 billion in Canadian currency) sale to the Canadian government in the spring.
"As we move ahead with the project and the purchase, our government remains committed to ensuring the project proceeds in a manner that protects the public interest". As there are no guarantees projects will be built, even after receiving regulatory and governmental approvals, Canada will be perceived as a less-reliable place for investment.
A second part of the ruling said the National Energy Board erred by not including marine tanker traffic in the scope of the project, thereby failing to consider the impact of oil tankers on southern resident killer whales under endangered species legislation.
The court decision is a victory for indigenous leaders and environmentalists, who have pledged to do whatever necessary to thwart the pipeline, including chaining themselves to construction equipment.
In 2013, Trans Mountain submitted an application to the National Energy Board for the Trans Mountain expansion project, stating that the primary goal of the project is to provide additional capacity to transport crude oil from Alberta to markets in the Pacific Rim, including Asia.
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Some First Nations, including Lower Nicola, had expressed interest in discussing with Ottawa about buying a stake in the pipeline. In 2016, Canada reached an agreement with all provinces except Saskatchewan to implement a national climate plan.
The Trans Mountain project isn't dead, but it's on life support.
"Certainly it is something that will no longer be top of mind for British Columbians", he said.
"Water is life. Water is sacred", he said, adding the federal government "never ever ever got our consent" for the pipeline.
Ian Anderson, president of Kinder Morgan Canada, issued the following statement: "We are reviewing the decision with the Government of Canada and are taking the appropriate time to assess next steps".
Vancouver Mayor Gregor Robertson said the decision validates his city's concerns about marine impacts and Indigenous consultation.
Cheam Chief Ernie Crey has been one of the most vocal supporters of the project, saying it would cost B.C. First Nations hundreds of millions of dollars in benefits, job training, and employment and business opportunities, if Trans Mountain was cancelled.
The environmental groups involved in the case also cheered the ruling, with Ecojustice, the Living Oceans Society and the Raincoast Conservation Foundation calling it a "critical win" for the climate and coastal ecosystems.
"Going forward, we urge politicians and other project proponents to shift their focus away from projects that lock us into dependence on fossil fuels", Ecojustice lawyer Dyna Tuytel said. "It's about the rule of law". "The court decision was not a condition of the transaction between KML and the federal government". Though enthusiasm for that move appears to have waned after the court ruling.