Antarctic Intermediate Water typically ranges from 500 to 1500 metres below the surface and is fed by melting Antarctic sea ice during the summer.
The water acts as a "climate buffer" and absorbs and redistributes excess heat and a large share of human carbon dioxide emissions.
A study published in scientific journal Nature Climate Change has revealed the layer was kept healthy from 1995 to 2015 by Antarctic summer ice melts.
However it abruptly changes from 2016 to 2024, becoming saltier, denser and deeper in conjunction with record low Antarctic sea ice.
"It was quite surprising. This alteration is happening very quickly," study lead and University of Melbourne associate professor Bishakhdatta Gayen said.
"Since we have records in oceanography, we have never seen this water alter.
"It's a big signal, the ocean is altering (and) it looks like the ocean is changing even faster than we thought."
The last big "switch" of the layer occurred at the end of the previous interglacial period, around 130,000 years ago when there was very little ice in the Antarctic.
"That transition took thousands of years, not two decades," Associate Professor Gayen said, adding it could lead to longer-lasting changes to the climate in the southern hemisphere.
The study analysed data from a network of 4000 robotic floats that sample the upper oceans as well as satellite and atmospheric information.
It didn't look at the environmental impact of the changes, or make projections.
However, study authors said a weaker layer could push more excess heat deeper into the ocean, meaning models may have underestimated deep-ocean warming and regional sea-level rises.
Co-author Professor Alberto Naveira Garabato said weather and the extent of storms in the southern hemisphere could be impacted and the effects could cascade globally.
A sustained change in the layer could feed into the Atlantic Meridional Overturning Circulation - the deep-ocean current system often linked to climate stability in the North Atlantic, he said.
Monash University Antarctic researcher Ariaan Purich said the far-reaching impacts of Antarctic sea ice loss were starting to be observed.
"Continued ocean observations combined with modelling are needed to better understand and adapt to the global consequences of low Antarctic sea ice," Dr Purich said.
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