Moreton Bay, seen from Moreton Island.
Moreton Bay's waterways will die within 20 years if more isn't done to protect the health of the bay, a leading Australian water scientist has warned.
Water sciences professor at Griffith University Jon Olley made the warning at the release of the 13th annual Healthy Waterways River Health findings on Wednesday.
Despite improvements in some river catchments, the scorecard for Moreton Bay showed the environmental health of the bay had worsened over the past year.
Professor Olley, a member of the Australian Rivers Institute and the Healthy Waterways Scientific Panel, said the health of central bay declined from an A-minus to a C-plus over 12 months, while Bramble Bay, near Redcliffe, dropped from a D grade to a fail grade of F.
"We are killing the bay, yes. It's a big statement to make, but yes, we are slowly killing the bay," he said.
Professor Olley said Moreton Bay would switch from a "seagrass environment" to an "algal environment", with a completely changed marine ecosystem in 20 years if nothing changed.
"Last year I reported that we were surprised as a group of scientists that the seagrass beds and the corals appeared to have improved slightly," he said.
"Well this year I am sorry to report that the seagrass beds and the corals are now showing signs of stress and decline and it is happening because of the large amounts of material that is being delivered to the bay from the catchments.
"We should be concerned about it."
Brisbane City Council is about to start pollution filtration trials in Oxley, Kedron, Norman and Toowong creeks.
But Professor Olley said more needed to be done.
He said he was concerned with mud flowing downstream from the Lockyer Valley as well as coming from constructions sites around Brisbane into Moreton Bay.
Mud is now flowing out to Moreton Bay 10 times as fast as it did before Europeans settled in the region 120 years ago.
"We need to put in place ways of improving the water quality coming out of the stormwater system and monitoring what is coming off construction sites," he said.
Environment Minister Andrew Powell said he was concerned about farmer's topsoil from the Lockyer Valley ending up in Moreton Bay.
Mr Powell also said the Queensland government would fund work by Healthy Waterways to tighten compliance by construction crews to halt soil being eroded from building sites.
"One of the things the government is committing to to providing funding to Healthy Waterways to work with councils around compliance," Mr Powell said, adding some developers were being innovative in controlling erosion.
However Fairfax Media has learned spot checks by Healthy Waterways show just 6 per cent of construction crews meet councils' erosion guidelines. In 2011, it was "zero per cent'.
Professor Olley said there was political will to make the changes.
"We have very good support among some of the senior politicians and I think that the more than people hear about the problems, the more they get behind the program," he said.
Professor Olley said persuading local councils to invest $1 billion to upgrade sewerage plants in the Brisbane Valley was now showing benefits.
"The value in the estuaries that was receiving sewage discharge used to be about seven times above the Queensland water standards," he said.
"They are now about two times the Queensland water standard."
Moreton Bay now supports tourism, industry, fishing and port facilities valued at $5 billion.