Climate change could lead to a 24 percent reduction in fish species and more storms, which could damage aquaculture farms and sink fishing boats.
This worst case scenario was laid out in a report sponsored by the largely business-backed think tank, Aotearoa Circle.
It looked at the position New Zealand's commercial fishers could find themselves in by 2050.
A best-case scenario was based on global warming being kept below 2 degrees Celcius, the level agreed on by most countries at the 2016 Paris Agreement, and a worst case scenario on it exceeding 4C.
Under a 4C scenario, acidification of the waters around New Zealand was predicted to increase by 150 percent.
"The implications for farmed shellfish are dire, with growth rates and productivity greatly diminished," according to the authors.
The increasing frequency of damaging storms sends insurance premiums ever higher and an increase in ocean temperatures makes some fish, such as hoki and ling, harder to find.
"Vessels must spend longer at sea, travel further, trawl at greater depth, and incur higher fuel and crew costs in order to target them."
On the upside, warmer waters will mean snapper and kingfish migrate to South Island fishing grounds, providing a boon to fishers there.
The picture looks brighter if the world manages to hold temperatures below 2 degrees.
By 2050 the report talks of "conspicuous conservation" and the fishing industry having achieved carbon neutrality.
"Global species abundance declines by around 10 percent but New Zealand fares much better than most, with net primary production in the oceans around New Zealand remaining broadly unchanged, and commercial catches holding up well."
However, acidification is still on the rise, increasing by 30 percent.
This pushes fin fish farms further offshore in search of cooler waters which in turn makes them a more expensive proposition.
"Global production of farmed fish surpasses the volume of wild capture fisheries for human consumption in the mid-2020s and is around 30 percent greater by the 2030s."
Other risks identified for the sector in this country were the growing popularity of plant-based proteins and the food miles debate pushing consumers towards food from closer to home, with a lower carbon footprint.
Just which scenario came to pass was an open question, however the report did point to analysis from the United Nations in 2019 that said the world was currently on track for more than 3 degrees of warming, even if all countries met their commitments under the Paris Agreement.
It warned the next 10 years were crucial.
"If we haven't taken decisive action by then, feedbacks and tipping points in the climate system will choose a perilous path for us."