Municipalities owe South Africa's water boards R1.1-billion, Water Affairs Minister Edna Molewa said on Wednesday.

Briefing the media at Parliament ahead of debate in the National Assembly on her department's budget vote, she said while this did not look good, it was "just about" 10% of the boards' annual revenue.

"Water board debt is about R1.1-billion. It's a lot of money, but the water boards' income per annum is over R8.8-billion. That's the revenue collection," Molewa said.

"So we're really looking at income levels and money owed. I'm not trying to suggest that [the debt situation] is not bad, but given that we are able to collect... over R8-billion... this debt is just about 10% of that."

It is understood the R1.1-billion figure the minister gave is the arrears debt, that is older than 60 days.

Molewa said her department was "engaging" with municipalities, and some were now paying their outstanding amounts.

She said a decision would be taken "in a few weeks" to re-align water boards and the areas they served, a plan which included the possibility of "cross-subsidisation" among these entities.