Federal parliamentary secretary for the environment, Senator Simon Birmingham, said Mr Knowles had played a valuable role in working towards a balanced and consultative approach in the development of the Basin Plan.

"Craig was appointed to take on a difficult task at a time of great disparity about what the Basin Plan should look like and considerable uncertainty about the ability to even achieve an agreed Basin Plan," Mr Birmingham said.

"Over his four years as chairman, Craig has placed a great emphasis on involving local communities and stakeholders in, firstly, the development of the Basin Plan and, subsequently, its implementation.

"Craig's approach to working with stakeholders, communities and basin governments ensured a plan that included a range of opportunities and options for governments to consider, build on, adapt and finally reach consensus."

Mr Knowles said he had enjoyed his time in the role and felt he had achieved what he had set out to do.

"I came into this role with the challenge of taking the MDBA through a process and delivering a Basin Plan to the Australian parliament in what has been, for more than 100 years, an extremely challenging and important area of public policy," Mr Knowles said.

"Seeing the Australian Parliament give such strong bipartisan support to the Basin Plan in 2012 was an important historical moment and a moment that is now being recognised internationally."

He said his remaining months would be focused on working with MDBA staff to finalise key pieces of work under the Basin Plan, and meeting with basin community and industry contacts.

An appointment of a new chairman will be made in due course, consistent with the requirements of the Water Act.