Flooding from ex-tropical cyclone Oswald earlier this year has taken its toll on Moreton Bay, off Brisbane, with its overall grade in a declining slightly from B- to C.
The Healthy Waterways annual report card ranks the health of south-east Queensland rivers and estuaries from A to F.
Waterways' spokesman Professor Jon Olley says reduced water clarity and increased algae in Moreton Bay are a direct result of mud and nutrients deposited during the 2011 and 2013 floods.
The central part of Moreton Bay declined the most from A- to C+.
Professor Olley also says the report also shows a decline in seagrass beds and coral in Moreton Bay.
"This year I'm sorry to report the seagrass beds and the corals are now showing signs of stress and decline, which is what we predicted would happen," he said.
State Environment Minister Andrew Powell says farmers have also had an impact on the health of waterways.
"We need to work with them, through incentives, through grants programmes to ensure we get a great environmental outcome," he said.
The Redlands catchment recorded an F, down from D-.
However, Professor Olley had good news for the Bremer River, which flows through Ipswich.
"The Bremer going from an F to a D-," he said.
"That's only the second time in 13 years of monitoring that the Bremer hasn't rated an F."
The Noosa, Tingalpa, Eprapah and Albert estuaries also improved.
© ABC 2013
11:55 EST New South Wales residents living near swollen waterways have been advised to stock up on essentials as forecasters warn flooding could isolate parts of the state later this week.