Toxic black sludge in Mandurah's fragile Peel-Harvey estuary has reached levels unseen anywhere else in the world, research has found, amid suggestions the Dawesville Cut is failing to alleviate algal growth and nutrient build-up.
And a separate investigation has found the estuary is returning to the state it was in before the $57 million cut was created, and warns its rehabilitation is unlikely under existing management.
Almost 20 years after the completion of the Dawesville Cut, designed to flush out algae and excessive nutrients, the waterways are plagued by toxic algal blooms and sulphidic black sediment.
A four-year study funded by the Australian Research Council, to be completed next year, has uncovered unprecedented levels of black sulphidic ooze, which can cause deoxygenation and lead to fish deaths.
Lead researcher Richard Bush, from Southern Cross University, said the rapid development in the region was a contributor to the build-up of black sediment and phosphorous, caused by fertilisers.
"It's an incredibly toxic material that is accumulating very fast. The concentration of sulphide exceeds any of the reported levels we've seen in similar environments across the world," he said.
Professor Bush said the Dawesville Cut "definitely doesn't seem to have fixed the problem in terms of toxic sediments".
A separate report, to be released by Murdoch University in conjunction with CSIRO, WA Marine Science Institution and WA Fisheries, found the health of the estuary was at a "critical juncture" and action was needed to prevent further decline.
Sarah Metcalf, from Murdoch's school of management and governance, said housing values, tourism and recreation were at stake as the condition deteriorated.
The report highlighted flaws in the management of the estuary, with overlapping jurisdictions and fragmented administration resulting in "weak or non-existent" monitoring.
Jan Star, chairwoman of the Peel-Harvey Catchment Council, said the estuary was being neglected. "The pressure to put more urban development down there is only going to increase the nutrient load going into the river," she said.
Department of Water science branch manager Malcolm Robb said the problem was in the upper reaches of the estuary, near the Murray and Serpentine rivers.
Substantially less flushing from the rivers contributed to the nutrient loads. Marine scientists were investigating reports of increased black mud and algae.
"Livestock grazing, dairies, horticulture, urban development and septic tanks all contribute to the problem of nutrient loading," Mr Robb said.