Scientists have raised concerns about another sting in the tail from Cyclone Debbie, with fresh runoff pollution from torrential rains sweeping into Great Barrier Reef waters where many corals lie smashed.

The cyclone dumped much of its deluge on a stretch of the north Queensland coast known as an “erosion hotspot” that generates almost a third of all sediment flowing into the reef.

Andrew Brooks, an associate professor at Griffith University, released pictures hinting at the scale of damage in the erosion-prone Burdekin catchment, as well as flood plumes from the Burdekin, Fitzroy and Gregory rivers pushing sediment and nitrogen pollution out to sea.

Brooks, in a helicopter flight partly funded by the federal and Queensland governments, flew over the area to gauge the damage on 31 March, three days after the cyclone hit.

The Fitzroy river mouth before and after the cyclone. In the top image the plume of sediment can be seen. Photograph: WWF

Brooks said the cyclone’s impact on a 11,000 sq km stretch of the Burdekin, estimated to produce 30% of runoff to the reef, highlighted the importance of a major state government investment in tackling erosion and improving land use in the area.

It comes after many coral reefs in the Whitsundays, which were largely spared mass bleaching further north, were pummelled and broken by Debbie.

Flood waters created a sweeping brown veil of sludge 18.5km out to sea from the mouth of the Burdekin, while the plume from the Gregory wrapped around Middle Island, 70 nautical miles south-east of Mackay.

Large alluvial gullies in Burdekin catchment. Photograph: Andrew Brooks/Griffith University/WWF

In the Burdekin, the collapse of a 20-metre bank was one of the signs of Debbie compounding problems in four river gully systems that have emerged as major sources of runoff.

These four gully systems covering 43 hectares alone had produced an estimated 36,000 tonnes of sediment a year for 60 years after being opened up amid cattle grazing and road building, Brooks said.

“Erosion from this hotspot must be significantly reduced to protect the reef,” he said.

“We know sediment can harm coral and sea grass by restricting light. Now we’re learning that sediment from this area also carries large loads of harmful nitrogen because it sticks to the sediment sourced from these same soils.”

Brooks said he hoped state and federal governments continued to take erosion in the area seriously as a health issue for the reef by funding rehabilitation of the area.

Sean Hoobin of WWF-Australia said the flood plume and erosion images were a concern after the reef was weakened by coral bleaching for an unprecedented two years in a row.

“We need greater investment in catchment repair so that the next cyclone or flood does less harm to the reef,” Hoobin said.