Flood waters are bringing the first major test of the northern projects of the Murray-Darling Basin Plan since it was struck in 2012.

Huge amounts of water from floods and dam releases are flowing through southern Queensland and into northern New South Wales, leaving many waiting to see who will be able to divert it as it makes its way south.

Queensland and South Australia are the only states whose Murray-Darling Basin plans have been accredited by the Commonwealth, meaning the Department of Natural Resources has set rules for diversion flood waters.

Cotton Australia chairman Hamish McIntyre says water resource plans finalised last year may now be tested.

“They haven't had many opportunities to work, and for us then to reflect on how they are working,” he said.

“[It will test] if they are meeting the critical human needs up front for our regional towns through to the environment and on to entitlement holders — whether it be irrigators or the great work floods do on the flood plains for grazing.”

The Murray-Darling Basin Authority says it is watching.

“The MDBA is watching this water closely via satellite as it heads into the heart of the Basin, through land still parched in some areas,” said Murray-Darling Basin Authority chief executive Philip Glyde

“This takes collaboration and trust,” he said.

Mr Glyde says Queensland irrigators are taking water from the flow only once they are permitted.

“Credit is also due to the New South Wales Government for imposing wide-ranging embargoes on water extraction in order to protect these first flows, as they had agreed to do. However, downstream water users were confused and raised some criticisms in relation to the partial lifting of the embargoes and these decisions were not transparent for all to see,” he said.

“We look forward to the New South Wales Government putting forward water resource plans that build these protections into their rules, providing confidence and transparency for all.

“This is the Basin Plan in action,” he said.