But an expert has warned the river's pristine condition could be short-lived.

Griffith University professor of water science and Australian Rivers Institute director Jon Olley said the Brisbane River is recuperating.

"We haven't had significant rain for a while now and whenever we don't have rain in the catchments, the river cleans up quite a bit," he said.

Professor Olley said it was well documented tremendous amounts of sediment and mud were washed downstream from the Lockyer Valley and Upper Brisbane River catchments in both the 2011 and 2013 floods.

That mud had been washed downstream into Moreton Bay, Professor Olley said.

"If you look at areas now there were completely muddy at the time – the Kangaroo Point beach is a good example – it was completely covered in mud," he said.

"Well that is now clean sand."

Professor Olley said riverside residents would notice it appeared cleaner because silt and mud had now washed through the river system.

"I live at Teneriffe and there were mud banks over most of the rock areas and now most of the mud has now gone," he said.

The Lower Brisbane River catchment around the inner-city area rated a C minus in the 2015 Healthy Waterways rivers report, with the next report due in November.

Healthy Waterways and Catchments chief executive Julie McLellan said last year's report card revealed the lower Brisbane catchment to be in fair environmental condition, but sediment from upstream remained the city's Achilles heel.

"Our monitoring identified good riparian vegetation and fair estuarine water quality," she said.

"But we do know that sediment runoff from rural and urban areas remains a critical issue.

"Over 50,000 dump trucks worth of sediment enters the region's waterways each year."

Professor Olley said future problems are now emerging beneath the waters of Moreton Bay.

"It has cleaned itself up well since the floods, but the sad part of the story is that all of the deep holes in Moreton Bay that were taking the fine sediment are now largely full," he said.

That means big problems for Moreton Bay when the next flood system emerges.

"Future floods will have a much larger impact on the (Moreton) Bay system," he said.

Professor Olley Griffith University postgraduate students have identified five major "deep holes" near St Helena Island in Moreton Bay which are now full.

He said that despite well-meaning talk and comments, little work had been done to control erosion in the Brisbane River catchments and a $500 million, 10-year revegetation plan was needed.

The pro-active, December 2014 Resilient Rivers policy by the previous state government, with the Council of Mayors (South East Queenland), which tried to invest $4.5million annually into catchment management, appears to have stopped.

"It hasn't been done and there is very little rehabilitation work that has been done in the catchment," he said.

"And when the next flood event comes through we will see large amounts of sediment delivered back into the estuary and the bay again."

Professor Olley said while South East Queensland Catchments, which had merged with Health Waterways, and the Green Army teams had delivered some programs, more riverside revegetation was needed.

"You are talking tens of kilometres that has been done, when you are talking about 6000 kilometres of rehab that is needed," he said.

However, Healthy Waters and Catchments general manager of science and solutions Craig Miller said water quality problems were not going to be solved overnight, but praised the early revegetation work underway.

"The reality is that the work that has been done throughout the catchments is seeing improvements," Dr Miller said.

He said work had started with graziers to improve "sustainable grazing lands management" in the Lockyer Creek and Upper Brisbane and Bremer river catchments.

"So you are getting better grass cover and it is also holding the sediment," he said.