The RSPCA says research has shown duck numbers fall when water levels rise steeply, creating unfavourable conditions in bird habitats.
"We believe it would be wise for the government to take a precautionary approach and not call a 2023 duck shooting season," animal welfare advocate Rebekah Eyers said.
"This will allow them to conduct an impact analysis and collect data on duck numbers following the flooding event."
This year's hunting season will run from March 18 to June 25 and allow for the shooting of five duck species - the grey teal, chestnut teal, Pacific black duck, Australian shelduck and the maned duck - with a daily bag limit of eight.
The season also allows for the shooting of quail with a 25-daily bag limit.
The peak in flooding down the Murray this week reached the Lower Lakes near the river mouth, south of Adelaide.
Recent surveys in those areas, including Lake Alexandrina, reported sightings of few water birds.
Further upstream, water flows across the SA border have fallen to about 135 gigalitres a day, down from a high of more than 190GL.
They are expected to drop to about 60GL a day by the end of January.
So far the bulk of the state's levee system have held up, including those protecting major assets such as the one at Renmark built near the local hospital, and another at Mannum protecting businesses on the main street.
There have been 68 catastrophic levee failures and 168 major problems but most have been with structures protecting agricultural lands.
The State Emergency Service will continue daily inspections across the levee network paying particular attention to those at Woods Point, Monteith, Jervois and River Glen.
Emergency Services Minister Joe Szakacs said some concerns remain for the integrity of major levees.
"By no stretch are we out of the woods. These levees continue to be under load," he said.
"There remains small but not insignificant risks about scarring, cracking and failing."
