Murray-Darling Basin Authority executive director Les Roberts said tight political deadlines imposed on the basin plan meant "large slabs" of the river system would remain unmapped by credible environmental science.

The basin plan, central to the Commonwealth's $12.9 billion Murray River takeover, will set extraction limits and new arrangements for water management. The draft plan will be released in June next year.

A year of consultation will follow before the plan is enacted in mid-2011, and Mr Roberts said those time frames would ensure "plenty of uncertainty" in the planning and knowledge available.

"It needs to be done in the blink of an eyelid, we have a political commitment for the basin plan to be made in 2011," he said.

"The timing to prepare the proposed basin plan essentially means there is no capacity for further research or new work in developing the plan. We have to rely on what is already available."

Speaking at a water debate in Melbourne yesterday, Mr Roberts said plenty of research was available on economic and social factors, but much less on environmental factors.

"In terms of environmental information, it is very patchy … there are large slabs of the basin where there is very limited information," he said. "I have to be absolutely clear about this; there'll be plenty of uncertainty."

Mr Roberts said most of the environmental science available was focused on high-profile assets such as Victoria's Barmah Forest.