The bloom of the microalgae, karenia mikimotoi, was identified off South Australia's Fleurieu Peninsula in March, and grew to more than 4400 sq km, close to the size of Kangaroo Island.
It has been breaking up in recent weeks, spreading north into Spencer Gulf, south into the Coorong wetlands and along Adelaide's beaches in Gulf St Vincent.
SA Environment Minister Susan Close said the "devastating" bloom had now been detected in Adelaide's Port River.
"Karenia mikimotoi has appeared in the Port River and is at reasonably high concentrations around Garden Island and Outer Harbour," she told reporters on Tuesday.
"Nothing near like the concentrations that we saw at the beginning of this bloom ... but nonetheless elevated amounts."
Ms Close said the algae had killed tens of thousands of marine animals from almost 400 species, and authorities were concerned some may be wiped out in the region.
"Although not toxic to humans, it is toxic to anything with gills and anything that seeks to breathe underwater, and we have seen just the beginnings of the extent of the devastation that's occurred under the sea," she said.
Port River is home to the Adelaide Dolphin Sanctuary but the dolphins are not believed to be at immediate risk from the algae because they are mammals.
But they may experience an allergic reaction or chose to leave the area because of the drop in fish numbers, Ms Close said.
SA Primary Industries and Regional Development Minister Clare Scriven said the government had started talks with the Commonwealth about recovery assistance.
It is not possible for the federal government to declare the incident a national disaster because the definition does not currently include algal blooms, she said.
The SA government announced backdated licence fee relief for commercial fishers, aquaculture and charter boat operators impacted by the bloom.
About $500,000 worth of fees will be waived to help operators, with a promise that more help will be available if needed.
SA Professional Fishers Association chair Ben Barnes said some fishers reported seeing "absolute destruction of the environment" and the industry was yet to see the worst of the disaster.
"They can't find fish, and it just doesn't seem to be clearing for them," he said.
"It will be a recurring thing that we just won't know for the next five to six years.
Mr Barnes said the "extent of the devastation" was unknown and the algae would likely have an impact on marine species reproduction.
Experts believe there are three potential contributing factors causing the bloom.
One is a marine heatwave that started in September 2024, with sea temperatures about 2.5C warmer than usual, combined with calm conditions, light winds and small swells.
Another is the 2022/23 River Murray flood that washed extra nutrients into the sea.
That was followed by an unprecedented cold-water upwelling in summer of 2023/24 that brought nutrient-rich water to the surface.
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