The federal government needs to invest $6 million over two years to kickstart a co-ordinated framework to deliver the reef's first cross-state biodiversity health check, Great Southern Reef Foundation co-founder Stefan Andrews says.
This should be followed by a $40 million, 10-year integrated monitoring program, co-designed with governments, First Nations, science and community partners.
"This is the most extensive marine mortality recorded in South Australia," Mr Andrews said while giving evidence on the first day of a senate inquiry into the ecological disaster.
"At least 500 species recorded from tens of thousands of citizen scientist shoreline observations, yet we still don't know the true underwater impacts because biodiversity monitoring is underfunded and fragmented.
"With robust monitoring, we can track impacts, guide recovery and safeguard biodiversity, fisheries, tourism and communities. Without it, we're flying blind."
The foundation had written to then environment minister Tany Plibersek in October 2023, warning marine heatwaves would impact the reef, which stretches from Kalbarri in Western Australia to the NSW-Queensland border.
"That initial letter, the specific requests (for funding), were not addressed," Mr Andrews said in Adelaide on Tuesday.
"The follow-up letter to (current Environment Minister) Murray Watt was in response to the early impacts of the harmful algal bloom, and it was again calling for the $40 million co-ordinated monitoring program."
"To date, there's been no commitment."
The inquiry is taking evidence from scientists, environmentalists, government representatives, tourism and fishing industry figures and recreational bodies.
It is seeking solutions to the bloom, which has spread to an area covering 4500 sq km since being identified off the Fleurieu Peninsula in March.
The SA and federal government have so far committed a $28 million package to respond to the bloom, including support for affected industries.
Charlie Huveneers, who is the director of Flinders University's Marine and Coastal Research consortium, said SA had been unprepared to deal with the algal bloom.
"At present, we cannot even assess the true impact of these kinds of events on our marine ecosystems because we lack the necessary baseline data and consistent monitoring programs," Dr Huveneers said.
"How can we tell you what has changed if we do not even know what it was, what was there to begin with?"
Monitoring in Australia's southern waters was "largely ad hoc and fragmented" and SA needed a joint consortium or marine institute to facilitate a more co-ordinated approach, he said.
"Such a framework would ensure that when extreme events occur, we have the capability, expertise and data to respond effectively without stronger monitoring, planning and collaboration," he said.
In other evidence, the SA government's algal bloom response co-ordinator, Chris Beattie, said the strategy for tackling the bloom in summer was still being developed, but "there'll be no intention on closing beaches from a public health perspective".
SA Health's principal water quality adviser David Cunliffe said brevetoxin had been detected in the foams off Adelaide beaches last week, so they had expanded advice to the public to include potential impacts.
"The modification we've now added is that asthmatics should have their medication available. It is not going to have long-term impacts on anybody," Dr Cunliffe said.
The inquiry will also sit in Port Lincoln, Ardrossan and Victor Harbor this week, and in Canberra on September 24.
The committee's report is due on October 28.
