Environment minister Sussan Ley said on Sunday the "spectacular start" for the state-of-the-art icebreaker had "turned a 39-day commissioning and resupply mission into a voyage of international discovery".
The canyon was 2200m below the surface of the Southern Ocean, 2000m wide and at least 55km long, while the undersea mountain was "taller than Mount Kosciuszko".
Water from the canyon was sampled using a conductivity, temperature and depth instrument used to measure changes in water properties, including ocean temperature and salinity near glaciers.
It will help researchers understand how warming water contributes to glacial melt from below.
"The Nuyina is allowing our Antarctic scientists to do things they simply haven't had the capacity to do before and underlines our commitment to world-leading Antarctic science," Ms Ley said.
Funding for the ship described as a "Disneyland for scientists" because of its cutting edge equipment designed to understand more about climate change, totals around $2 billion over 30 years.
Acoustic instruments mounted within the hull of Nuyina's drop keel, including a multibeam echosounder were used to map the seafloor, throughout the voyage.
The information will add to global efforts to chart the world's oceans by 2030.
The $529 million vessel also used a wet-well, a watertight compartment that can process 5000 litres of sea water a minute, to capture thousands of Antarctic krill "in perfect condition for researchers to study".
Apart from its scientific discoveries, Nuyina successfully pumped almost a million litres of fuel to sub-Antarctic research station Casey to keep it running, and delivered helicopters and supplies to another, Davis.
It will depart on its second voyage to Davis and Macquarie Island in early February.
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