Police were told the man went missing about 1.30pm on Monday in floodwaters near Casson Ave at Loxton North on the Murray River, south of Berri.
"The search is expected to continue until last light and will resume tomorrow morning," SA Police said.
South Australian State Emergency Service crews are assisting police in the search along with interstate resources, an SES spokesman told AAP.
Peak flows have also reached Mannum, east of Adelaide, closing a major ferry crossing on Monday, with river heights expected to continue into the Lower Lakes by the end of the week.
The rising river will likely close the Tailem Bend ferry within days, causing transport issues for a significant number of residents.
That will bring the number of closures to 11. The remaining two ferries, at Cadell and Narrung, are also likely to cease operations by mid-January.
The Tailem Bend closure will turn what was previously a 10-minute exercise to cross the river into an 80km round trip to access the road crossing at Murray Bridge.
In response, the state government has approved a one-off $300 payment to low-income earners, pensioners, concession card holders, job seekers and students to help cover the extra travel costs.
Qualifying reasons include attending medical appointments, work, volunteering, collecting essential supplies or attending to carer duties.
Treasurer Stephen Mullighan said the measure was expected to cost the government up to $3 million.
"It's an important commitment for us to make sure people can stay mobile in these communities," he said.
"The last thing we want is for people to feel like they can't go about their daily lives because of these rising floodwaters."
Premier Peter Malinauskas said even without the flood, the cost of fuel was a significant burden for low and fixed-income households.
"The closure of roads and ferries has made it even tougher for some in river communities to get to the shops, attend appointments and care for friends and family," he said.
"This one-off payment is a recognition of that fact."
As water levels begin to recede ferry services will resume but there are no fixed dates at this stage.
The premier said the ferry at Lyrup, in the Riverland, would logically be the first to reopen.
He said when ferries could be put back in operation was often dependent on other issues, such as the safety of the road approaches, and not just water levels.
The Murray flooding has impacted about 3400 properties in SA, including nearly 400 primary residences.
It has also closed more than 120 roads across the river communities.
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