But a lot of the water damage to this season's 593,000 hectare planting has not been from flooding.

Rather it has been the unusually cool temperatures and bouts of persistent damp weather that have eroded yield prospects.

Although generally great for growing grass and fattening livestock, the rainy summer has caused its fair share of grief for large scale croppers and horticulture producers in both States.

Mild temperatures have widely delayed cotton plant growth and disrupted flowering, while a wet fortnight on the Queensland's Central Highlands caused widespread boll rot.

The extent of this week's flood damage to about 62,000ha of cotton in the southern Queensland's St George and Lower Balonne River system is not likely to be realised until late this week.

Water spilling west from Beardmore Dam and into irrigation areas downstream has added to pressure from surging river levels between St George and Dirranbandi.

"It's impossible to say what it will look like, but it's certainly unlikely to be anything like the fantastic season in that catchment last year," said Queensland Cotton (QC) managing director Richard Haire.

Last year QC, which has a gin at Dirranbandi and two at St George, processed about 500,000 bales from the area, which includes the giant Cubbie Station cotton crop, which again spreads over more than 20,000ha this season.

Mr Haire expected this season's forecast national 4.9 million bale harvest to probably shrink to around 4.5m bales because of delays at planting, mixed growing conditions and the impact of flooding and prolonged wet weather.

"Things can change, but the general feeling is that across the board the yield per hectare is not going to be as much as last year," he said.

"Parts of the Namoi and Gwydir valleys and St George area have been hurt pretty hard by flooding, but the wet conditions have certainly not as bad as last year for other regions like the Darling Downs."

The big winner could be the yield from an estimated 123,000ha of dryland crop in NSW and Queensland said Cotton Australia's Queensland policy officer, Michael Murray.

"Generally overcast weather hasn't been conducive to cotton growing, but there's a lot of dryland country that has been well watered this summer, including about 35,000ha of the (total 98,000ha) Downs crop," he said.