The Opposition says Ombudsman Richard Bingham has agreed to look into its claims of incompetence over a $46 million bonus paid to the builder of Adelaide's desalination plant.

Opposition water spokesman Mitch Williams says AdelaideAqua was given the bonus under its contract with SA Water despite failing to meet deadlines.

He says SA Water has refused to release documents about the payment.

"I've been trying to get hold of these documents since early this year," he said.

"I've been through a lengthy process under the freedom of information laws and John Ringham, the head of SA Water, confirmed that he didn't want to release the documents.

"That's why I've gone to the Ombudsman and if I don't get satisfaction from the Ombudsman, I will take it to the courts."

Water Minister Paul Caica says the bonus was built into the overall cost of the water filtration project and was a contractual arrangement between SA Water and AdelaideAqua.

"There has certainly been some money provided to AdelaideAqua. Part of that payment provided for an extra shift, that in turn had the benefit of ensuring that there was safety on site, but also that we were able to complete what was a major change on the scope of the project from 50 gigalitres to 100 gigalitres," he said.