The central and south-east Queensland cotton industry is facing multi-million dollar losses from flooding and there is more rain on the way.

The Dawson river at Theodore west of Bundaberg rose to 13 metres on Friday night inundating cotton crops.

Grower David Moore says he has lost about 400 hectares.

"[That] could possibly be upwards of a million dollars worth of cotton," he said.

He says it could take more than five years to recover from the losses.

Now there is a new threat.

Rain last night to the north has seen the river rise to seven metres at Taroom.

Dawson Valley Cotton Growers Association spokeswoman Fleur Anderson says growers downstream are worried the river levels will climb even higher.

"It'll be down in Theodore in probably three days," she said.

Ms Anderson says it could mean more damage to crops by the end of the week.