The river has been dropping at Renmark by about six gigalitres a day for the past three days, State Emergency Services chief Chris Beattie said.
"We're confident this indicates the peak has passed," he told reporters on Tuesday.
"All of our gauges downstream from Renmark continue to show rises and we'll expect to see that outlook continue for the next two-and-a-half to three weeks as the peak flows through."
The flood levee held up at Renmark but the downstream Mypolonga levee was breached on Monday and it could be overtopped in the coming days, Mr Beattie said.
The Bolto community, about 100 kilometres east of Adelaide, is also isolated after the levee at Mannum was breached.
Authorities will continue to do welfare checks to ensure the remaining Bolto residents are safe, Mr Beattie said.
Three adults and a child had to be rescued from flood waters on Monday after their boat failed near Blanchetown.
The group had been returning to collect furniture from their property when their vessel sank and they had to cling to trees.
"The near miss is a timely reminder of the dangers of the river," Mr Beattie said.
"I encourage all people that have to use the river either for work or to access a property to be very mindful of the restrictions."
All non-essential activity on the Murray has been banned including boating, fishing and swimming, and multiple ferry services remain suspended.
More than 3000 houses and properties remain without power, with more disconnections expected.
SA Premier Peter Malinauskas on Tuesday announced $10,000 grants for small businesses, farm enterprises and not-for-profit organisations affected by the floods.
The grants will be available to those businesses along the river who have experienced a downturn of 30 per cent over a three-month period.
"We're hopeful that all businesses will survive beyond the floods," Mr Malinauskas told reporters on Tuesday.
Meanwhile, ex-tropical cyclone Ellie continues to dump intense rain on the Northern Territory's vast Barkly region, with Alexandria Downs Station recording 156mm of rain in the 24 hours to 9am Tuesday.
The weather system has started moving northwest and is expected to track close to Tennant Creek on Wednesday morning before intensifying in the Gregory district and Kimberley region later in the week.
Despite the change of direction, authorities warn that life-threatening flash flooding remains possible, with 24-hour rainfall totals up to 250mm and damaging winds forecast for some areas.
A severe weather warning and flood warning remains in place for various rivers and catchments in the northwestern, central and southern NT.
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