The CSIRO has told a world aquaculture conference in Adelaide the industry already is facing challenges from climate change.
The fast-growing industry generates more than $1 billion annually for the Australian economy and CSIRO research scientist Alistair Hobday says aquaculture operators have been making a strong impression in the international marketplace.
"I think aquaculture operators in Australia are very sophisticated, they grow high-value products that go to international markets as well as our domestic markets and I think they're well set up for coping with these changes," he said.
But Dr Hobday says aquaculture operators will need to find ways to adapt to rising temperatures.
"We've seen cases around Australia where warming waters that have been unusually warm have led to declines in salmon production, have led to declining oxygen in tuna pens," he said.
The CSIRO says temperatures have risen by one degree Celsius in the past century in Australia, but by more than two degrees in the south-east and south-west of the nation.
It predicts a further rise of two to three degrees by 2050, a rate faster than for the rest of the world.
Interstate moves are likely
Dr Hobday thinks some aquaculture industries will need to move states to ensure species are bred in suitable temperatures.
"I think we'll see farmers growing a different mix of species, but because the Australian seafood industry is very well integrated, instead of you as a consumer purchasing your barramundi from Queensland, you'll be purchasing it from the Barossa Valley," he said.
Also at the global conference, Ros Harvey of Sense-T says the industry is making increasing use of technology, such as using a sensor to monitor the health of oysters.
"They can accumulate biotoxins which make them dangerous to eat, so by using data and very clever models we can actually only shut when we need to and be able to predict when we're going to shut and that's really important for industry, so they can get product out to market," she said.
The Federal Government has committed to boosting the industry, releasing a national aquaculture statement at the conference.
It outlines a commitment from the Government to build an efficient and sustainable industry.
Agriculture Minister Richard Colbeck says cutting back the administrative processes in the aquaculture industry will help.
"There are a few roadblocks that exist I think in respect of some planning and approval processes and if we can make them more streamlined and easy for industry to work through, I think that it will benefit," he said.
"[There are] a range of things that need to operate at a state level rather than at a Commonwealth level so all of these things can be considered as part of this process and give the industry and government a good sense of what needs to be done to continue to grow this industry, which has huge opportunity here in Australia."
The Federal Government says a next step will be to release a strategy for the aquaculture industry.