The Victorian Environmental Water Holder has moved to clear up concerns it operates to different entitlement rules than irrigators.
During the last few wet years, it's been claimed water spilled from dams, to create airspace, is not being deducted from environmental accounts.
But Victorian Environmental Water Holder Andrew Sharpe said that wasn't the case.
"We have the same rules, by and large, as everyone else in the system who have similar sorts of entitlements," Mr Sharpe said.
He said the environmental water holders lost water that spilled, in the same way irrigators did.
"Depending on the size of the spill, some of the water we carry over is quarantined until Goulburn-Murray Water declares a low risk of spill and if a spill happens, we will lose that water," he said.
"That's the same as private irrigators with similar sorts of entitlements and in similar sorts of conditions."
Water spills if the dams fill up and the storage space is needed for inflows to support allocations.
Mr Sharpe said most of the environmental water in northern Victoria was held by the Commonwealth Environmental Water Holder, with the VEWH co-ordinating its release.
"Most of their entitlements came from the purchase of private entitlements, and when they were purchased all the conditions associated with those entitlements were transferred directly across," he said.
"Whatever the conditions were associated with that water, when it was in private hands, are exactly the same, now it is in the hands of the environmental water holder."
He said the water held by the VEWH and CEWH in the dams was only a "very small proportion of what the environment needed.
"The water we hold fills the gaps in whatever else happens in the environment - if we were going to have a system where the water we held provided everything the environment needs, we would need many times the volume of water we have got," he said.
"The entitlements set aside for the environment are based on the assumption natural floods will happen - we are supplementing, filling the gaps, in between those natural events."
Mr Sharpe said while it was true in three of the last six years, environmental bodies had carried over about the same amount of water as irrigators in the Victorian Murray system, the VEWH looked at the whole of the north.
"If you look at across the whole northern portfolio coming into this year, we carried over about 765 gigalitres and private water holders carried over 1,265GL, so it's 500GL more carried over in the private sector," he said.
"We also did an analysis of the proportion of held entitlement, in the last couple of years we have been carrying over similar proportions."
He believed greater understanding was required of the role of the VEWH.
"We basically manage all the held environmental water entitlements, in Victoria, held in reservoirs and we oversee and co-ordinate its release for environmental outcomes," Mr Sharpe said.
That included fish breeding, supporting water birds and wetlands, and restoring floodplain restoration.
"I get why people see it and say that's unfair, or 'this is different' - the main thing we all need to do is have an open discussion," he said.
'Hopefully, through that, we get a greater awareness - we are conscious of how people on the land are feeling, both from flood risk, then in dry times when they are thinking about their allocations."