The Department of Environment and Water says it is hard to tell whether the Queensland floods will affect River Murray flows in South Australia.
The coordinator of River Murray operations, Jarrod Eaton, says most of the rain has fallen on the eastern side of the Great Dividing Range.
He says there will also be an influx of water at the top end of the Darling River.
However, Mr Eaton says most of that will be used before it reaches the Menindee Lakes.
"General rule of thumb, we generally see about 75 per cent of the water being consumed ... there's long travel times, something like 2,000 kilometres from some of those rivers in Queensland, just down to the Menindee Lakes," he said.
"You have obviously irrigation diversion along the way, we have quite expansive flood plains, so we typically can see large volumes of water being lost."
Mr Eaton says most of the water will flow into the ocean, rather than the Murray-Darling system.
"A lot of those larger rainfalls and inflows into the river there are on the wrong side of the divide, so on the eastern side of the Great Dividing Range," he said.
"However, there has been some rainfall over the last couple of days on the western side of the divide which is resulting in some major, moderate and minor flooding in a number of rivers across Queensland and New South Wales."
© ABC 2013
16:06 EST The weather bureau has implemented a new system of forecasting the seasonal outlook called Predictive Ocean Atmosphere Model for Australia, or POAMA.