The Murray-Darling Basin Authority has met to discuss the recent criticism over water-sharing and has declared some plans put forward would place drinking water at risk for some regional towns.
In a communique, it declared many people misunderstood water arrangements, confusing the state-based water sharing plan that had been in place for over 100 years with the MDBA Plan.
It defended its role in maintaining environmental flows during the drought.
It also sent a strong warning to NSW over its refusal to complete water sharing plans until the drought was over, saying this will throw the whole Murray-Darling system into confusion and possibly leave water users at the mercy of Commonwealth and other states' interests.
"The Authority were concerned about the continued commentary opposing the use of water for the environment during this drought," the communique said.
"Under the Water Act, the security of water for the environment is the same as for any other water user.
"The Basin Plan was designed to ensure that when water has been allocated, the environmental water holder could continue to use their water without interference or pressure. This water is vital to keep the rivers healthy, which benefits everyone.
"There have also been questions raised about making available the water held in conveyancing reserves in the storages of the Snowy River Hydro scheme.
"This water must be reserved for next year to be able to supply and deliver towns and communities with drinking water if the drought continues.
"Claims that the reserves should be released now would put these towns at risk.
"We learned from the Millennium Drought that we need to plan in advance for the coming year. The Authority wants communities to have a secure water supply. The provision of critical human water needs is a cornerstone of the Basin Plan and that means water for people above all other interests."
The Murray-Darling Basin Authority met in Canberra earlier this week over two days just as more than 3000 farmers and stakeholders descended on the capital to protest at the plan, saying rural communities were being ruined by the plan, and at the lack of access to water, which they declared was their constitutional right.
The Authority though said the debate was confused.
"The Authority noted that many of the expressed concerns arise from the way water is managed and shared between Basin states and allocated within each state. These arrangements should not be confused with the Basin Plan.
"For more than 100 years, the states have been sharing the waters of the River Murray in accordance with water sharing rules and arrangements set out in the Murray-Darling Basin Agreement, not the Basin Plan. Historically, significant changes have only been made to this Agreement under exceptional circumstances."
The MDBA said it welcomed Water Minister David Littleproud's announcement of a new investigation to be led by Interim Inspector General of Murray-Darling Basin Water Resources Mick Keelty.
He is due to report by the end of March next year, and will examine how changing patterns of river inflows and water use have affected state shares under the Agreement, and "the reserves that are required by the Agreement and how they impact on state water shares and subsequent water allocation policies".
The MDBA rounded down on the demands released this week by the NSW Government, which has refused to hand over any more water to the plan.
"NSW is required to submit all water resource plans by the end of 2019 but recent public comments from NSW Ministers suggest that submission of their water resource plans may be deferred until after the drought has broken," the MDBA said.
"If this happens, it will only create greater uncertainty and confusion for water users who would then be subject to both Commonwealth and State legislation, which is not clearly aligned. The Authority emphasised that water resource plans are live instruments and can continue to be adapted and refined through time."
The MDBA urged all parties to see through the plan.
"The Authority strongly encouraged all Basin governments to remain committed to the Basin Plan and work together in partnership to sustainably manage the water resources of the Murray-Darling Basin. Members acknowledged that communities are battling one of the worst droughts on record. However, the reform remains a once in a life time opportunity to restore and protect the health of this great river system for the long-term benefit of all basin communities."
Meantime the Nature Conservation Council said NSW Premier Gladys Berejiklian should reaffirm her government's commitment to the Murray-Darling Basin Plan.
"The National Party needs to stop playing politics with water and get on with delivering the Murray-Darling Basin Plan," NCC Chief Executive Chris Gambian said.
"Changing water policy in the midst of a drought crisis is a recipe for failure. We must stick to the plan and NSW must honor its end of the bargain to make it work. The Murray-Darling Basin Plan is imperfect, but it is far better than anything else on offer."