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Thanks to AAP for this accurate report.

In documents tendered to the Federal Court on Thursday, opponents of the Port Phillip Bay dredge argue the project has ballooned since it was first referred to the federal government for consideration in early 2002.

They are seeking to overturn federal Environment Minister Peter Garrett's approval - granted just before Christmas - in a last ditch bid to stop the dredger moving in next month.

Michael Morehead, the lawyer for the opponents, the Blue Wedges Coalition, told the court Mr Garrett's approval was invalid because it was based on an "inadequate referral" made in 2002.

A 2007 assessment report had since increased the dredging depth from a maximum of two metres to an unspecified depth of at least five metres, he said.

"This has significant consequences both for the depth of dredging and the activities included within the scope of the proposed action," Mr Morehead said.

But lawyers for Mr Garrett, the Port of Melbourne Corporation (PoMC) and the Victorian government maintain the process is sound.

PoMC lawyer Greg Garde, QC, warned any delay in the project - which is set to start on February 1 - would cost the PoMC $1.7 million a week.

The project will dredge 23 million cubic metres of sea bed from the bay's shipping channels to allow larger vessels to dock in Melbourne.

Mr Morehead told the court the original report made no reference to the disposal of toxic sediment in the bay or a plume that would extend 8.33km into Bass Strait and a commonwealth marine area.

The report also did not consider the impact on all threatened species, including the Australian grayling fish, and the extent of the sites to be dredged, he said.

"Yet somehow they've found their way into this (2007) assessment," Mr Morehead said.

He referred to an analysis by Monash University ecologist Simon Roberts, who compared the two reports and concluded the project in its current form was "significantly larger in area, volume, depth and its likely impact".

"The amount of material to be dredged in the capital phase of the project is more than the equivalent of digging a two-metre deep by 15-metre wide trench from Melbourne to Sydney," Dr Roberts said in his report.

"This material will then be transported and dumped at two spoil grounds.

"If it were instead placed on the city of Melbourne (CBD) ... it would cover it to a depth of approximately 23 metres, the equivalent of a typical eight-storey building."

Lawyers for the other parties said it was normal for projects to evolve and every issue of national environmental significance had been thoroughly evaluated, as per the Environment Protection and Biodiversity Conservation Act.

The decision was Mr Garrett's and he had the power to request more information if required.

"The act does not fix any minimum context for the assessment," Mr Garrett's lawyer Peter Hanks, QC, told the court.

Justice Peter Heerey reserved his decision to a date to be fixed.