They are applying to have the court overturn an EPA report and subsequent ministerial decisions to approve the project, alleging apparent bias and failure to follow procedure.
Wilderness Society spokesman Peter Robertson says the court action was filed after the EPA's chairman Paul Vogel made the sole decision last July to approve the gas hub because all other board members had a perceived conflict of interest.
"The outcome that we're hoping for is that the Supreme Court will agree with us that the way that the EPA handled this fiasco was unlawful," he said.
"And, therefore any so-called approvals that arise from this should be overturned - that's what we're seeking."
The society says it hopes its Supreme Court challenge will result in a review of the environmental approvals of the $30 billion Kimberley gas hub.
The court heard this morning that Woodside Petroleum has applied to join the case affecting its proposed gas processing facility at the hub, north of Broome.
Woodside is arguing its legal rights are affected.
Mr Robertson says a sole person should not have made the EPA decision.
"We're also challenging the fact that once those conflicts of interest had been not only declared but acknowledged, instead of the Minister and the EPA following what we and others recommended which was that a separate panel of people be empanelled to carry out this assessment," he said.
"Instead of that, our views and other people's views were ignored and they went ahead and instead instead of having a minimum of three EPA board members they reduced it to just one member of the five member EPA board making the final decision.
"That is just a gross misuse of decision making processes of the EPA."
Mr Robertson says the legal challenge is expensive but feels it is his duty.
"[It's about] restoring some confidence and faith in the way that the EPA operates and the way it conducts it's environmental assessments," he said.
"If groups like us don't do things like this then they, the Government, will end up getting away with very shonky decision making processes and that can't be allowed to happen."
"When you see an independent statutory body being reduced to nothing more than basically a political facilitation agency for the government, then that's a very very sad state of affairs for Western Australia and for our environment and future generations.
"And, the Wilderness Society and the traditional owners are obviously very determined to make that those decision making processes aren't allowed to stand."
The EPA has declined to comment.
Woodside and the Minister have been contacted for comment.
A directions hearing on the matter will be heard on March 22.