Niwa oceanographer Mike William will lead a team of scientists using a suite of underwater cameras, moorings and sensors to study the changes to the ocean.
He said the site was ideal to study because it was a small region which had undergone a big change with potentially global implications - yet it was a small enough area to be studied in a single voyage.
"One of the aims of this voyage is to understand how the ice tongue breaking off has changed the polynya and hence how much dense water is formed there. We also hope to map the sea floor and reveal the area under the glacier tongue for the first time," Dr Williams said.
The research would help scientists understand how changes in polynyas would affect the flow in the deep ocean.
"By comparing the new measurements to previous observations, we will determine how the temperature, salinity and circulation of the Southern Ocean are changing," Dr Williams said.
There are seven New Zealand researchers on board, including five from Niwa, as well as a four French scientists, 11 Australian researchers and a crew of 16.
Australian research team leader Steve Rintoul said earlier research in the region had shown rapid changes were underway in the deep ocean - but scientists were not yet sure what was driving the changes.
"The measurements collected on the Tangaroa voyage will be used to test the hypothesis that increased melt of Antarctic ice is driving changes we see in the deep ocean."
The Tangaroa will take about eight days to reach the polynya, with scientists monitoring CO2 levels on the ocean surface and in the atmosphere on the way.
Samples will also be collected from deeper waters to see how much carbon is going into the deep ocean, which will provide insights into how CO2 is affecting the acidity of the ocean.
Geologists will also retrieve sedimentary cores from the sea floor using a long metal cylinder, which is lowered to the ocean floor and then pushed into the sediment under a heavy weight.
Niwa geologist Dr Helen Bostock said the sediment cores were "archives of past changes in the ocean".
"The data from cores provides clues as to how the ocean temperature, nutrients, biological productivity, and sea ice extent have changed over thousands of years."
The voyage is part of the research programme of the Antarctic Climate and Ecosystems Cooperative Research Centre, based in Hobart, of which Niwa is a core partner.